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<h1 class="epydoc">Source Code for <a href="trunk.BIP.Bayes.Samplers.MCMC-module.html">Module trunk.BIP.Bayes.Samplers.MCMC</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># To change this template, choose Tools | Templates</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"># and open the template in the editor.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">Module implementing MCMC samplers </tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-docstring">    - Metropolis: Adaptive Metropolis Hastings sampler</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-docstring">    - Dream: DiffeRential Evolution Adaptive Markov chain sampler</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pdb</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">cython</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">xmlrpclib</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">logging</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">multiprocessing</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Pool</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">random</tt> <tt class="py-keyword">import</tt> <tt class="py-name">sample</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">np</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">liveplots</tt><tt class="py-op">.</tt><tt class="py-name">xmlrpcserver</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Function trunk.BIP.Viz.realtime.rpc_plot()=trunk.BIP.Viz.realtime-module.html#rpc_plot"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-0', 'rpc_plot', 'link-0');">rpc_plot</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-name">mean</tt><tt class="py-op">,</tt><tt class="py-name">isnan</tt><tt class="py-op">,</tt>  <tt class="py-name">nan_to_num</tt><tt class="py-op">,</tt> <tt class="py-name">var</tt><tt class="py-op">,</tt> <tt class="py-name">sqrt</tt><tt class="py-op">,</tt> <tt class="py-name">inf</tt><tt class="py-op">,</tt> <tt class="py-name">exp</tt><tt class="py-op">,</tt> <tt class="py-name">greater</tt><tt class="py-op">,</tt> <tt class="py-name">less</tt><tt class="py-op">,</tt> <tt class="py-name">identity</tt><tt class="py-op">,</tt> <tt class="py-name">ones</tt><tt class="py-op">,</tt> <tt class="py-name">zeros</tt><tt class="py-op">,</tt> <tt class="py-name">floor</tt><tt class="py-op">,</tt> <tt class="py-name">log</tt><tt class="py-op">,</tt> <tt class="py-name">recarray</tt><tt class="py-op">,</tt> <tt class="py-name">nan</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">random</tt> <tt class="py-keyword">import</tt> <tt class="py-name">random</tt><tt class="py-op">,</tt>  <tt class="py-name">multivariate_normal</tt><tt class="py-op">,</tt>  <tt class="py-name">multinomial</tt><tt class="py-op">,</tt>  <tt class="py-name">rand</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt> <tt class="py-keyword">import</tt> <tt class="py-name">cov</tt><tt class="py-op">,</tt>  <tt class="py-name">uniform</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt><tt class="py-op">,</tt> <tt class="py-name">scoreatpercentile</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-name">__author__</tt><tt class="py-op">=</tt><tt class="py-string">"fccoelho"</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-name">__date__</tt> <tt class="py-op">=</tt><tt class="py-string">"$09/12/2009 10:44:11$"</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC.logger=trunk.BIP.Bayes.Samplers.MCMC-module.html#logger,Variable trunk.BIP.logger=trunk.BIP-module.html#logger,Variable trunk.BIP.logsetup.logger=trunk.BIP.logsetup-module.html#logger"><a title="trunk.BIP.Bayes.Samplers.MCMC.logger
trunk.BIP.logger
trunk.BIP.logsetup.logger" class="py-name" href="#" onclick="return doclink('link-1', 'logger', 'link-1');">logger</a></tt> <tt class="py-op">=</tt> <tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">getLogger</tt><tt class="py-op">(</tt><tt class="py-string">'BIP.MCMC'</tt><tt class="py-op">)</tt> </tt>
<a name="timeit"></a><div id="timeit-def"><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="timeit-toggle" onclick="return toggle('timeit');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC-module.html#timeit">timeit</a><tt class="py-op">(</tt><tt class="py-param">method</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="timeit-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="timeit-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">    Decorator to time methods</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt class="py-keyword">def</tt> <tt class="py-def-name">timed</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kw</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">        <tt class="py-name">ts</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">        <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">method</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">kw</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-name">te</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">'%r  %2.2f sec'</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">              <tt class="py-op">(</tt><tt class="py-name">method</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> <tt class="py-op">,</tt> <tt class="py-name">te</tt><tt class="py-op">-</tt><tt class="py-name">ts</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
</div><a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">timed</tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"> </tt>
<a name="_Sampler"></a><div id="_Sampler-def"><a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="_Sampler-toggle" onclick="return toggle('_Sampler');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html">_Sampler</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  </tt>
</div><a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-docstring">'''</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">    Base classe for all samplers</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">    Holds common logic and </tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt id="link-2" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler._po=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_po"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-2', '_po', 'link-2');">_po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt id="link-3" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler._dimensions=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_dimensions"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._dimensions" class="py-name" href="#" onclick="return doclink('link-3', '_dimensions', 'link-3');">_dimensions</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> <tt class="py-comment">#cache for dimensions</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt id="link-4" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#trace_acceptance"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance" class="py-name" href="#" onclick="return doclink('link-4', 'trace_acceptance', 'link-4');">trace_acceptance</a></tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt id="link-5" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_convergence=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#trace_convergence"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_convergence" class="py-name" href="#" onclick="return doclink('link-5', 'trace_convergence', 'link-5');">trace_convergence</a></tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt id="link-6" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#seqhist"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-6', 'seqhist', 'link-6');">seqhist</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt id="link-7" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#liklist"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-7', 'liklist', 'link-7');">liklist</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt id="link-8" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler.e=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#e"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-8', 'e', 'link-8');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1e-20</tt> <tt class="py-comment">#very small number used in the proposal covariance function calculation</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt id="link-9" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler._j=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_j"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._j" class="py-name" href="#" onclick="return doclink('link-9', '_j', 'link-9');">_j</a></tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt id="link-10" class="py-name" targets="Variable trunk.BIP.Bayes.Samplers.MCMC._Sampler._R=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_R"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._R" class="py-name" href="#" onclick="return doclink('link-10', '_R', 'link-10');">_R</a></tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt> <tt class="py-comment">#Gelman Rubin Convergence</tt> </tt>
<a name="_Sampler.__init__"></a><div id="_Sampler.__init__-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="_Sampler.__init__-toggle" onclick="return toggle('_Sampler.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt>  <tt class="py-param">parpriors</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  <tt class="py-param">parnames</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.__init__-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt> <tt class="py-op">=</tt> <tt class="py-name">parpriors</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt> <tt class="py-op">=</tt> <tt class="py-name">parnames</tt> </tt>
</div><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="_Sampler.best_prop_index"></a><div id="_Sampler.best_prop_index-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="_Sampler.best_prop_index-toggle" onclick="return toggle('_Sampler.best_prop_index');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#best_prop_index">best_prop_index</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.best_prop_index-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.best_prop_index-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">        Returns the index of the best fitting proposal, i.e.,</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">        the one which with max Likelihood</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-11', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-12', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-13', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="_Sampler.DIC"></a><div id="_Sampler.DIC-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="_Sampler.DIC-toggle" onclick="return toggle('_Sampler.DIC');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#DIC">DIC</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.DIC-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.DIC-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">        Calculates  the deviance information criterion</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-name">D</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-14', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-name">Dbar</tt> <tt class="py-op">=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">D</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-name">meanprop</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-name">pd</tt> <tt class="py-op">=</tt> <tt class="py-name">Dbar</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld._output_loglike()=trunk.BIP.Bayes.Melding.Meld-class.html#_output_loglike"><a title="trunk.BIP.Bayes.Melding.Meld._output_loglike" class="py-name" href="#" onclick="return doclink('link-15', '_output_loglike', 'link-15');">_output_loglike</a></tt><tt class="py-op">(</tt><tt class="py-name">meanprop</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likfun</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">        <tt id="link-16" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#DIC"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-16', 'DIC', 'link-16');">DIC</a></tt> <tt class="py-op">=</tt> <tt class="py-name">pd</tt> <tt class="py-op">+</tt><tt class="py-name">Dbar</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-17" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-17', 'DIC', 'link-16');">DIC</a></tt> </tt>
</div><a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="_Sampler.dimensions"></a><div id="_Sampler.dimensions-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="_Sampler.dimensions-toggle" onclick="return toggle('_Sampler.dimensions');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#dimensions">dimensions</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.dimensions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.dimensions-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._dimensions" class="py-name" href="#" onclick="return doclink('link-18', '_dimensions', 'link-3');">_dimensions</a></tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._dimensions" class="py-name" href="#" onclick="return doclink('link-19', '_dimensions', 'link-3');">_dimensions</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._dimensions" class="py-name" href="#" onclick="return doclink('link-20', '_dimensions', 'link-3');">_dimensions</a></tt> </tt>
</div><a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="_Sampler.po"></a><div id="_Sampler.po-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="_Sampler.po-toggle" onclick="return toggle('_Sampler.po');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#po">po</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.po-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.po-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring">        Pool of processes for parallel execution of tasks</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">        Remember to call self.term_pool() when done.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-21', '_po', 'link-2');">_po</a></tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-22', '_po', 'link-2');">_po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-23', '_po', 'link-2');">_po</a></tt><tt class="py-op">.</tt><tt class="py-name">_state</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-24', '_po', 'link-2');">_po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#Pool has been terminated</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-25', '_po', 'link-2');">_po</a></tt> </tt>
</div><a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"> </tt>
<a name="_Sampler.shut_down"></a><div id="_Sampler.shut_down-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="_Sampler.shut_down-toggle" onclick="return toggle('_Sampler.shut_down');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#shut_down">shut_down</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">reason</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.shut_down-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.shut_down-expanded"><a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring">        Finalizes the sampler, nicely closing the resources allocated</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"><tt class="py-docstring">            - `reason`: comment stating why the sampling is being shutdown.</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.term_pool()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#term_pool"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.term_pool" class="py-name" href="#" onclick="return doclink('link-26', 'term_pool', 'link-26');">term_pool</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">OSError</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method trunk.BIP.Viz.realtime.RTplot.close_plot()=trunk.BIP.Viz.realtime.RTplot-class.html#close_plot"><a title="trunk.BIP.Viz.realtime.RTplot.close_plot" class="py-name" href="#" onclick="return doclink('link-27', 'close_plot', 'link-27');">close_plot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.close_plot" class="py-name" href="#" onclick="return doclink('link-28', 'close_plot', 'link-27');">close_plot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">reason</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">            <tt id="link-29" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.logger
trunk.BIP.logger
trunk.BIP.logsetup.logger" class="py-name" href="#" onclick="return doclink('link-29', 'logger', 'link-1');">logger</a></tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">(</tt><tt class="py-name">reason</tt><tt class="py-op">)</tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"> </tt>
<a name="_Sampler.term_pool"></a><div id="_Sampler.term_pool-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="_Sampler.term_pool-toggle" onclick="return toggle('_Sampler.term_pool');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#term_pool">term_pool</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.term_pool-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.term_pool-expanded"><a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-30', '_po', 'link-2');">_po</a></tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-31', '_po', 'link-2');">_po</a></tt><tt class="py-op">.</tt><tt class="py-name">_state</tt><tt class="py-op">:</tt> <tt class="py-comment">#Pool needs terminating</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-32', '_po', 'link-2');">_po</a></tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-33', '_po', 'link-2');">_po</a></tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._po" class="py-name" href="#" onclick="return doclink('link-34', '_po', 'link-2');">_po</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"> </tt>
<a name="_Sampler.gr_R"></a><div id="_Sampler.gr_R-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="_Sampler.gr_R-toggle" onclick="return toggle('_Sampler.gr_R');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#gr_R">gr_R</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.gr_R-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.gr_R-expanded"><a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._j" class="py-name" href="#" onclick="return doclink('link-35', '_j', 'link-9');">_j</a></tt> <tt class="py-op">==</tt> <tt class="py-name">end</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._R" class="py-name" href="#" onclick="return doclink('link-36', '_R', 'link-10');">_R</a></tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.gr_convergence()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#gr_convergence"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.gr_convergence" class="py-name" href="#" onclick="return doclink('link-37', 'gr_convergence', 'link-37');">gr_convergence</a></tt><tt class="py-op">(</tt><tt class="py-name">end</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._j" class="py-name" href="#" onclick="return doclink('link-38', '_j', 'link-9');">_j</a></tt> <tt class="py-op">=</tt> <tt class="py-name">end</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._R" class="py-name" href="#" onclick="return doclink('link-39', '_R', 'link-10');">_R</a></tt> </tt>
</div><a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"> </tt>
<a name="_Sampler.gr_convergence"></a><div id="_Sampler.gr_convergence-def"><a name="L140"></a><tt class="py-lineno">140</tt> <a class="py-toggle" href="#" id="_Sampler.gr_convergence-toggle" onclick="return toggle('_Sampler.gr_convergence');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#gr_convergence">gr_convergence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">relevantHistoryEnd</tt><tt class="py-op">,</tt> <tt class="py-param">relevantHistoryStart</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.gr_convergence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.gr_convergence-expanded"><a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-docstring">        Gelman-Rubin Convergence</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">relevantHistoryStart</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-name">relevantHistoryEnd</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">        <tt class="py-name">N</tt> <tt class="py-op">=</tt> <tt class="py-name">end</tt> <tt class="py-op">-</tt> <tt class="py-name">start</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">N</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._R" class="py-name" href="#" onclick="return doclink('link-40', '_R', 'link-10');">_R</a></tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt><tt class="py-op">*</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">        <tt class="py-name">N</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-41', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">N</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">        <tt class="py-name">seq</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-42', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">N</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">        <tt class="py-name">sequences</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt> <tt class="py-comment">#this becomes an array (nchains,samples,dimensions)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-name">variances</tt>  <tt class="py-op">=</tt> <tt class="py-name">var</tt><tt class="py-op">(</tt><tt class="py-name">sequences</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-comment">#array(nchains,dim)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">        <tt class="py-name">means</tt> <tt class="py-op">=</tt> <tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">sequences</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-comment">#array(nchains,dim)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt class="py-name">withinChainVariances</tt> <tt class="py-op">=</tt> <tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">variances</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">        <tt class="py-name">betweenChainVariances</tt> <tt class="py-op">=</tt> <tt class="py-name">var</tt><tt class="py-op">(</tt><tt class="py-name">means</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">N</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-name">varEstimate</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt> <tt class="py-op">-</tt> <tt class="py-number">1.0</tt><tt class="py-op">/</tt><tt class="py-name">N</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">withinChainVariances</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">/</tt><tt class="py-name">N</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">betweenChainVariances</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._R" class="py-name" href="#" onclick="return doclink('link-43', '_R', 'link-10');">_R</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">varEstimate</tt><tt class="py-op">/</tt> <tt class="py-name">withinChainVariances</tt><tt class="py-op">)</tt> </tt>
</div><a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line"> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">np</tt><tt class="py-op">.</tt><tt class="py-name">vectorize</tt> </tt>
<a name="_Sampler._accept"></a><div id="_Sampler._accept-def"><a name="L161"></a><tt class="py-lineno">161</tt> <a class="py-toggle" href="#" id="_Sampler._accept-toggle" onclick="return toggle('_Sampler._accept');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_accept">_accept</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">last_lik</tt><tt class="py-op">,</tt>  <tt class="py-param">lik</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler._accept-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler._accept-expanded"><a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"><tt class="py-docstring">        Decides whether to accept a proposal</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">last_lik</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">last_lik</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">inf</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-comment"># liks are logliks</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">lik</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-name">inf</tt><tt class="py-op">:</tt><tt class="py-comment">#0:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">last_lik</tt> <tt class="py-op">&gt;</tt><tt class="py-op">-</tt><tt class="py-name">inf</tt><tt class="py-op">:</tt><tt class="py-comment">#0:</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">            <tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt> <tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">-</tt><tt class="py-name">last_lik</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">            <tt class="py-comment">#alpha = min(lik-last_lik, 1)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">last_lik</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-name">inf</tt><tt class="py-op">:</tt><tt class="py-comment">#0:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">            <tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Negative likelihood!?!"</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-comment">#        print "last_lik, lik, alpha: ",  last_lik, lik, alpha</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">alpha</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"> </tt>
<a name="_Sampler.setup_xmlrpc_plotserver"></a><div id="_Sampler.setup_xmlrpc_plotserver-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="_Sampler.setup_xmlrpc_plotserver-toggle" onclick="return toggle('_Sampler.setup_xmlrpc_plotserver');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#setup_xmlrpc_plotserver">setup_xmlrpc_plotserver</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.setup_xmlrpc_plotserver-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.setup_xmlrpc_plotserver-expanded"><a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-docstring">        Sets up the server for real-time chain watch</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">        <tt class="py-name">p</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt id="link-44" class="py-name" targets="Function trunk.BIP.SDE.gillespie.p2()=trunk.BIP.SDE.gillespie-module.html#p2"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-44', 'p2', 'link-44');">p2</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">p</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">or</tt> <tt id="link-45" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-45', 'p2', 'link-44');">p2</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-46', 'rpc_plot', 'link-0');">rpc_plot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">            <tt id="link-47" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-47', 'p2', 'link-44');">p2</a></tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="trunk.BIP.Viz.realtime.rpc_plot" class="py-name" href="#" onclick="return doclink('link-48', 'rpc_plot', 'link-0');">rpc_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">hold</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver</tt> <tt class="py-op">=</tt> <tt class="py-name">xmlrpclib</tt><tt class="py-op">.</tt><tt class="py-name">ServerProxy</tt><tt class="py-op">(</tt><tt class="py-string">'http://localhost:%s'</tt><tt class="py-op">%</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt> <tt class="py-op">=</tt> <tt class="py-name">xmlrpclib</tt><tt class="py-op">.</tt><tt class="py-name">ServerProxy</tt><tt class="py-op">(</tt><tt class="py-string">'http://localhost:%s'</tt><tt class="py-op">%</tt><tt id="link-49" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-49', 'p2', 'link-44');">p2</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">         </tt>
<a name="_Sampler.shutdown_xmlrpc_plotserver"></a><div id="_Sampler.shutdown_xmlrpc_plotserver-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="_Sampler.shutdown_xmlrpc_plotserver-toggle" onclick="return toggle('_Sampler.shutdown_xmlrpc_plotserver');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#shutdown_xmlrpc_plotserver">shutdown_xmlrpc_plotserver</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.shutdown_xmlrpc_plotserver-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.shutdown_xmlrpc_plotserver-expanded"><a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver</tt><tt class="py-op">.</tt><tt class="py-name">flush_queue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver</tt><tt class="py-op">.</tt><tt class="py-name">shutdown</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt><tt class="py-op">.</tt><tt class="py-name">flush_queue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt><tt class="py-op">.</tt><tt class="py-name">shutdown</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">         </tt>
<a name="_Sampler._every_plot"></a><div id="_Sampler._every_plot-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="_Sampler._every_plot-toggle" onclick="return toggle('_Sampler._every_plot');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_every_plot">_every_plot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler._every_plot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler._every_plot-expanded"><a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"><tt class="py-docstring">        plotting function for generating a plot at every step</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div><a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"> </tt>
<a name="_Sampler._watch_chain"></a><div id="_Sampler._watch_chain-def"><a name="L206"></a><tt class="py-lineno">206</tt> <a class="py-toggle" href="#" id="_Sampler._watch_chain-toggle" onclick="return toggle('_Sampler._watch_chain');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_watch_chain">_watch_chain</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">j</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler._watch_chain-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler._watch_chain-expanded"><a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">j</tt><tt class="py-op">&lt;</tt><tt class="py-number">100</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.gr_convergence" class="py-name" href="#" onclick="return doclink('link-50', 'gr_convergence', 'link-37');">gr_convergence</a></tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">100</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Gelman-Rubin's R: "</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._R" class="py-name" href="#" onclick="return doclink('link-51', '_R', 'link-10');">_R</a></tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method trunk.BIP.Viz.realtime.RTplot.clearFig()=trunk.BIP.Viz.realtime.RTplot-class.html#clearFig"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-52', 'clearFig', 'link-52');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-name">thin</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt><tt class="py-op">//</tt><tt class="py-number">500</tt> <tt class="py-keyword">if</tt> <tt class="py-name">j</tt><tt class="py-op">//</tt><tt class="py-number">500</tt> <tt class="py-op">!=</tt><tt class="py-number">0</tt> <tt class="py-keyword">else</tt> <tt class="py-number">1</tt> <tt class="py-comment">#history is thinned to show at most 500 points, equally spaced over the entire range</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">        <tt class="py-name">chaindata</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">history</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">:</tt><tt class="py-name">thin</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt class="py-name">obs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">;</tt><tt class="py-name">lbs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">&gt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">                <tt class="py-name">obs</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">                <tt class="py-name">lbs</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">                <tt class="py-name">obs</tt> <tt class="py-op">+=</tt> <tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">                <tt class="py-name">lbs</tt> <tt class="py-op">+=</tt> <tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">chaindata</tt><tt class="py-op">,</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">chaindata</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">j</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">,</tt> <tt class="py-string">"Chain Progress."</tt><tt class="py-op">,</tt><tt class="py-string">'points'</tt> <tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">lbs</tt><tt class="py-op">,</tt> <tt class="py-string">"Fit"</tt><tt class="py-op">,</tt> <tt class="py-string">'points'</tt> <tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">        <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">50</tt> <tt class="py-keyword">if</tt> <tt class="py-number">3</tt><tt class="py-op">*</tt><tt class="py-name">j</tt><tt class="py-op">//</tt><tt class="py-number">4</tt><tt class="py-op">&lt;</tt><tt class="py-number">50</tt> <tt class="py-keyword">else</tt> <tt class="py-number">3</tt><tt class="py-op">*</tt><tt class="py-name">j</tt><tt class="py-op">//</tt><tt class="py-number">4</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">        <tt class="py-comment">#series = [self.phi[k][s:j].mean(axis=0).tolist() for k in self.data.keys()]</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">        <tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">        <tt class="py-name">bi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-53', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-54', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment">#index of the best fit</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">        <tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">        <tt class="py-name">best</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">bi</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">        <tt class="py-name">mlabels</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'Mean '</tt><tt class="py-op">+</tt><tt class="py-name">l</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">        <tt class="py-name">blabels</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'Best '</tt><tt class="py-op">+</tt><tt class="py-name">l</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">mlabels</tt><tt class="py-op">,</tt> <tt class="py-string">"Mean fit of last %s samples"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'lines'</tt> <tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">(</tt><tt class="py-name">best</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">blabels</tt><tt class="py-op">,</tt> <tt class="py-string">"mean and best fit of last %s samples"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'lines'</tt> <tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pserver2</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="trunk.BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-55', 'clearFig', 'link-52');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">        <tt class="py-comment">#TODO: Implement plot of best fit simulation against data</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line"> </tt>
<a name="_Sampler._tune_likvar"></a><div id="_Sampler._tune_likvar-def"><a name="L237"></a><tt class="py-lineno">237</tt> <a class="py-toggle" href="#" id="_Sampler._tune_likvar-toggle" onclick="return toggle('_Sampler._tune_likvar');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_tune_likvar">_tune_likvar</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ar</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler._tune_likvar-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler._tune_likvar-expanded"><a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">arhist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">ar</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tsig</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tstep</tt> <tt class="py-op">=</tt> <tt class="py-number">.05</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">arhist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">ar</tt><tt class="py-op">]</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">        <tt class="py-name">dev</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">0.35</tt><tt class="py-op">-</tt><tt class="py-name">ar</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dev</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0.02</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt> <tt class="py-op">*=</tt> <tt class="py-number">1</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tsig</tt> <tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">.5</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">tanh</tt><tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">*</tt><tt class="py-name">dev</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-comment">#ar at target, don't change anything</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">        <tt class="py-name">improv</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">0.35</tt><tt class="py-op">-</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">arhist</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-number">0.35</tt><tt class="py-op">-</tt><tt class="py-name">ar</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">improv</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tsig</tt> <tt class="py-op">*=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-comment">#change signal if AR is not improving</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tstep</tt> <tt class="py-op">=</tt> <tt class="py-number">.05</tt> <tt class="py-comment">#reset to small steps if changing direction</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">improv</tt>  <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">improv</tt> <tt class="py-op">&lt;</tt><tt class="py-number">.01</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt><tt class="py-number">.05</tt><tt class="py-op">:</tt> <tt class="py-comment">#1 in 20 chance to change direction if no improvements</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tsig</tt> <tt class="py-op">*=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-comment">#change signal if AR is not improving</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">improv</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0.01</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tstep</tt> <tt class="py-op">*=</tt> <tt class="py-number">0.97</tt> <tt class="py-comment">#reduce step if approacching sweet spot</tt> </tt>
</div><a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-comment">#    @np.vectorize</tt> </tt>
<a name="_Sampler.check_constraints"></a><div id="_Sampler.check_constraints-def"><a name="L259"></a><tt class="py-lineno">259</tt> <a class="py-toggle" href="#" id="_Sampler.check_constraints-toggle" onclick="return toggle('_Sampler.check_constraints');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#check_constraints">check_constraints</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">theta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler.check_constraints-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler.check_constraints-expanded"><a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line"><tt class="py-docstring">        Check if given theta vector complies with all constraints</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line"><tt class="py-docstring">            - `theta`: parameter vector</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line"><tt class="py-docstring">            </tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"><tt class="py-docstring">            True if theta passes all constraints, False otherwise</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">constraints</tt><tt class="py-op">:</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt id="link-56" class="py-name" targets="Variable trunk.BIP.SDE.example.r=trunk.BIP.SDE.example-module.html#r"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-56', 'r', 'link-56');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">constraints</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-57" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-57', 'r', 'link-56');">r</a></tt><tt class="py-op">.</tt><tt class="py-name">all</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">     </tt>
<a name="_Sampler._propose"></a><div id="_Sampler._propose-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="_Sampler._propose-toggle" onclick="return toggle('_Sampler._propose');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_propose">_propose</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">step</tt><tt class="py-op">,</tt> <tt class="py-param">po</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Sampler._propose-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Sampler._propose-expanded"><a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line"><tt class="py-docstring">        Generates proposals.</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line"><tt class="py-docstring">        returns two lists</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"><tt class="py-docstring">            - `step`: Position in the markov chain history.</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line"><tt class="py-docstring">            - `po`: Process pool for parallel proposal generation</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line"><tt class="py-docstring">            - `theta`: List of proposed self.dimensional points in parameter space</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"><tt class="py-docstring">            - `prop`: List of self.nchains proposed phis.</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">        <tt class="py-name">thetalist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">        <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line">        <tt class="py-name">initcov</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">identity</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#dimensions"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-58', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-59" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream.step()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#step,Method trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step()=trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#step"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-59', 'step', 'link-59');">step</a></tt> <tt class="py-op">&lt;=</tt> <tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-60', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">:</tt>  </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">                <tt class="py-comment">#sample from the priors</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">                <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">                    <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt><tt class="py-op">[</tt><tt class="py-name">dist</tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">dist</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">]</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.check_constraints()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#check_constraints"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.check_constraints" class="py-name" href="#" onclick="return doclink('link-61', 'check_constraints', 'link-61');">check_constraints</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">                        <tt class="py-keyword">continue</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">greater</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">less</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-62', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">                        <tt class="py-keyword">break</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> <tt class="py-op">=</tt> <tt class="py-name">initcov</tt> <tt class="py-comment">#assume no covariance at the beginning</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">                <tt class="py-comment">#use gaussian proposal</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-63" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-63', 'step', 'link-59');">step</a></tt><tt class="py-op">%</tt><tt class="py-number">10</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-64', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;=</tt><tt class="py-number">10</tt><tt class="py-op">:</tt> <tt class="py-comment">#recalculate covariance matrix only every ten steps</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">                    <tt class="py-name">cv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt><tt class="py-op">*</tt><tt class="py-name">cov</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-65', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">10</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-66', 'e', 'link-8');">e</a></tt><tt class="py-op">*</tt><tt class="py-name">identity</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-67', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> <tt class="py-op">=</tt> <tt class="py-name">cv</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">                    <tt class="py-name">cv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">                <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">                    <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">multivariate_normal</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-68', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">cv</tt><tt class="py-op">,</tt> <tt class="py-name">size</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">greater</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">less</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-69', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">                        <tt class="py-keyword">break</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">            <tt class="py-name">thetalist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-70" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.po()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#po"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-70', 'po', 'link-70');">po</a></tt><tt class="py-op">:</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">            <tt class="py-name">proplis</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-71" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-71', 'po', 'link-70');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt id="link-72" class="py-name" targets="Function trunk.BIP.Bayes.Melding.model_as_ra()=trunk.BIP.Bayes.Melding-module.html#model_as_ra,Function trunk.BIP.Bayes.Samplers.MCMC.model_as_ra()=trunk.BIP.Bayes.Samplers.MCMC-module.html#model_as_ra"><a title="trunk.BIP.Bayes.Melding.model_as_ra
trunk.BIP.Bayes.Samplers.MCMC.model_as_ra" class="py-name" href="#" onclick="return doclink('link-72', 'model_as_ra', 'link-72');">model_as_ra</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Function trunk.BIP.Bayes.Melding.model()=trunk.BIP.Bayes.Melding-module.html#model"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-73', 'model', 'link-73');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">thetalist</tt><tt class="py-op">]</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">            <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">job</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">job</tt> <tt class="py-keyword">in</tt> <tt class="py-name">proplis</tt><tt class="py-op">]</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">            <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-74" class="py-name"><a title="trunk.BIP.Bayes.Melding.model_as_ra
trunk.BIP.Bayes.Samplers.MCMC.model_as_ra" class="py-name" href="#" onclick="return doclink('link-74', 'model_as_ra', 'link-72');">model_as_ra</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-75', 'model', 'link-73');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">thetalist</tt><tt class="py-op">]</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">        <tt class="py-name">propl</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">proplist</tt><tt class="py-op">]</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">thetalist</tt><tt class="py-op">,</tt><tt class="py-name">propl</tt> </tt>
</div></div><a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line"> </tt>
<a name="Metropolis"></a><div id="Metropolis-def"><a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line"><tt class="py-comment">#TODO: remove dependency on the meld object</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <a class="py-toggle" href="#" id="Metropolis-toggle" onclick="return toggle('Metropolis');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html">Metropolis</a><tt class="py-op">(</tt><tt class="py-base-class">_Sampler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Metropolis-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Metropolis-expanded"><a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"><tt class="py-docstring">    Standard random-walk Metropolis Hastings sampler class</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="Metropolis.__init__"></a><div id="Metropolis.__init__-def"><a name="L325"></a><tt class="py-lineno">325</tt> <a class="py-toggle" href="#" id="Metropolis.__init__-toggle" onclick="return toggle('Metropolis.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">meldobj</tt><tt class="py-op">,</tt> <tt class="py-param">samples</tt><tt class="py-op">,</tt> <tt class="py-param">sampmax</tt><tt class="py-op">,</tt>  <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">,</tt> <tt class="py-param">parpriors</tt><tt class="py-op">,</tt> <tt class="py-param">parnames</tt><tt class="py-op">,</tt> <tt class="py-param">parlimits</tt><tt class="py-op">,</tt> <tt class="py-param">likfun</tt><tt class="py-op">,</tt> <tt class="py-param">likvariance</tt><tt class="py-op">,</tt> <tt class="py-param">burnin</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Metropolis.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Metropolis.__init__-expanded"><a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line"><tt class="py-docstring">        MCMC based fitting</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line"><tt class="py-docstring">            - `samples`: Number of samples to obtain</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line"><tt class="py-docstring">            - `sampmax`: Maximum number of samples drawn.</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: observed time series on the model's output</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line"><tt class="py-docstring">            - `t`: length of the observed time series</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line"><tt class="py-docstring">            - `parpriors`: Dictionary with frozen distributions objects as values and parnames as keys</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line"><tt class="py-docstring">            - `parnames`: List of parameter names</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line"><tt class="py-docstring">            - `parlimits`: list of tuples with (min,max) for every parameter.</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line"><tt class="py-docstring">            - `likfun`: Likelihood function</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line"><tt class="py-docstring">            - `likvariance`: variance of the Normal likelihood function</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line"><tt class="py-docstring">            - `burnin`: Number of burnin samples</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">salt_band</tt> <tt class="py-op">=</tt> <tt class="py-number">0.05</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt> <tt class="py-op">=</tt> <tt class="py-name">samples</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sampmax</tt> <tt class="py-op">=</tt> <tt class="py-name">sampmax</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt> <tt class="py-op">=</tt> <tt class="py-name">parpriors</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt> <tt class="py-op">=</tt> <tt class="py-name">parnames</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt> <tt class="py-op">=</tt> <tt class="py-name">parlimits</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likfun</tt> <tt class="py-op">=</tt> <tt class="py-name">likfun</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt> <tt class="py-op">=</tt> <tt class="py-name">likvariance</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt> <tt class="py-op">=</tt> <tt class="py-name">meldobj</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">t</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt> <tt class="py-op">=</tt> <tt class="py-name">burnin</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt>  </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">2.38</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-76', 'dimensions', 'link-58');">dimensions</a></tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-77', 'e', 'link-8');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1e-20</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">kwargs</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwargs</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">                <tt class="py-keyword">exec</tt><tt class="py-op">(</tt><tt class="py-string">'self.%s = %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt>  </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">        <tt class="py-comment"># Combined history of accepted samples</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">history</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-78', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">        <tt class="py-comment">#complete history of all chains as a dictionary with keys as integer ids of the chains</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-79', 'seqhist', 'link-6');">seqhist</a></tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">        <tt class="py-comment">#self.seqhist = np.zeros((self.nchains, self.dimensions, samples+self.burnin))</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.setup_xmlrpc_plotserver()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#setup_xmlrpc_plotserver"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.setup_xmlrpc_plotserver" class="py-name" href="#" onclick="return doclink('link-80', 'setup_xmlrpc_plotserver', 'link-80');">setup_xmlrpc_plotserver</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line"> </tt>
<a name="Metropolis._propose"></a><div id="Metropolis._propose-def"><a name="L368"></a><tt class="py-lineno">368</tt> <a class="py-toggle" href="#" id="Metropolis._propose-toggle" onclick="return toggle('Metropolis._propose');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#_propose">_propose</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">step</tt><tt class="py-op">,</tt> <tt class="py-param">po</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Metropolis._propose-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Metropolis._propose-expanded"><a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line"><tt class="py-docstring">        Generates proposals.</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line"><tt class="py-docstring">        returns two lists</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line"><tt class="py-docstring">            - `step`: Position in the markov chain history.</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line"><tt class="py-docstring">            - `po`: Process pool for parallel proposal generation</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line"><tt class="py-docstring">            - `theta`: List of proposed self.dimensional points in parameter space</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line"><tt class="py-docstring">            - `prop`: List of self.nchains proposed phis.</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line">        <tt id="link-81" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-81', 'po', 'link-70');">po</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line">        <tt class="py-name">thetalist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">        <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">        <tt class="py-name">initcov</tt> <tt class="py-op">=</tt> <tt class="py-name">identity</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-82', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">initheta</tt> <tt class="py-keyword">and</tt> <tt id="link-83" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-83', 'step', 'link-59');">step</a></tt> <tt class="py-op">&lt;=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">            <tt class="py-comment">#start from user-defined point in parameter space.</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">                <tt class="py-name">thetalist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">initheta</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> <tt class="py-op">=</tt> <tt class="py-name">initcov</tt> <tt class="py-comment">#assume no covariance at the beginning</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">                <tt class="py-name">off</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-84" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-84', 'step', 'link-59');">step</a></tt> <tt class="py-op">&lt;=</tt> <tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-85', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">:</tt>  </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line">                    <tt class="py-comment">#sample from the priors</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line">                    <tt class="py-keyword">while</tt> <tt class="py-name">off</tt><tt class="py-op">&lt;</tt><tt class="py-number">50</tt><tt class="py-op">:</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line">                        <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt><tt class="py-op">[</tt><tt class="py-name">par</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">par</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">]</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.check_constraints" class="py-name" href="#" onclick="return doclink('link-86', 'check_constraints', 'link-61');">check_constraints</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">                            <tt class="py-keyword">continue</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">t</tt><tt class="py-op">&lt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-87', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">:</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line">                            <tt class="py-keyword">break</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line">                        <tt class="py-name">off</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">off</tt> <tt class="py-op">==</tt><tt class="py-number">50</tt><tt class="py-op">:</tt><tt class="py-comment">#try a compromising proposal</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line">                        <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-88', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-comment">#last accepted proposal for this chain</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line">    <tt class="py-comment">#                print "off:" , off</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> <tt class="py-op">=</tt> <tt class="py-name">initcov</tt> <tt class="py-comment">#assume no covariance at the beginning</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line">                    <tt class="py-comment">#use gaussian proposal</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt id="link-89" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-89', 'step', 'link-59');">step</a></tt><tt class="py-op">%</tt><tt class="py-number">10</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-90', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;=</tt><tt class="py-number">10</tt><tt class="py-op">:</tt> <tt class="py-comment">#recalculate covariance matrix only every ten steps</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">                        <tt class="py-name">cv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt><tt class="py-op">*</tt><tt class="py-name">cov</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-91', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">10</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-92', 'e', 'link-8');">e</a></tt><tt class="py-op">*</tt><tt class="py-name">identity</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-93', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line">                        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> <tt class="py-op">=</tt> <tt class="py-name">cv</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">                        <tt class="py-name">cv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line">                    <tt class="py-comment">#print self.parlimits</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line">                    <tt class="py-keyword">while</tt> <tt class="py-name">off</tt><tt class="py-op">&lt;</tt><tt class="py-number">50</tt><tt class="py-op">:</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line">                        <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">multivariate_normal</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-94', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">cv</tt><tt class="py-op">,</tt> <tt class="py-name">size</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">t</tt><tt class="py-op">&lt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-95', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">:</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">                            <tt class="py-keyword">break</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line">                        <tt class="py-name">off</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">off</tt> <tt class="py-op">==</tt><tt class="py-number">50</tt><tt class="py-op">:</tt> <tt class="py-comment">#try a compromising proposal</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">                        <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-96', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-comment">#last accepted proposal for this chain</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line">                    <tt class="py-comment">#print "off:" , off</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line">                <tt class="py-name">thetalist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-97" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-97', 'po', 'link-70');">po</a></tt><tt class="py-op">:</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">            <tt class="py-name">proplis</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-98" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-98', 'po', 'link-70');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt id="link-99" class="py-name"><a title="trunk.BIP.Bayes.Melding.model_as_ra
trunk.BIP.Bayes.Samplers.MCMC.model_as_ra" class="py-name" href="#" onclick="return doclink('link-99', 'model_as_ra', 'link-72');">model_as_ra</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-100', 'model', 'link-73');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">thetalist</tt><tt class="py-op">]</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">            <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">job</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">job</tt> <tt class="py-keyword">in</tt> <tt class="py-name">proplis</tt><tt class="py-op">]</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line">            <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-101" class="py-name"><a title="trunk.BIP.Bayes.Melding.model_as_ra
trunk.BIP.Bayes.Samplers.MCMC.model_as_ra" class="py-name" href="#" onclick="return doclink('link-101', 'model_as_ra', 'link-72');">model_as_ra</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-102', 'model', 'link-73');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">thetalist</tt><tt class="py-op">]</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">        <tt class="py-name">propl</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">proplist</tt><tt class="py-op">]</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">thetalist</tt><tt class="py-op">,</tt><tt class="py-name">propl</tt> </tt>
</div><a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line"> </tt>
<a name="Metropolis.step"></a><div id="Metropolis.step-def"><a name="L431"></a><tt class="py-lineno">431</tt> <a class="py-toggle" href="#" id="Metropolis.step-toggle" onclick="return toggle('Metropolis.step');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#step">step</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt>  <tt class="py-param">nchains</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Metropolis.step-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Metropolis.step-expanded"><a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line"><tt class="py-docstring">        Does the actual sampling loop.</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">        <tt class="py-name">ptheta</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-103', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">)</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line">        <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">rej</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">ar</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment">#total samples,accepted samples, rejected proposals, acceptance rate</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line">        <tt class="py-name">last_lik</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-name">j</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">current_step</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">stop_now</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.shut_down()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#shut_down"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.shut_down" class="py-name" href="#" onclick="return doclink('link-104', 'shut_down', 'link-104');">shut_down</a></tt><tt class="py-op">(</tt><tt class="py-string">'user interrupted'</tt><tt class="py-op">)</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line">            <tt class="py-comment">#generate proposals</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line">            <tt class="py-name">theta</tt><tt class="py-op">,</tt><tt class="py-name">prop</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Metropolis._propose()=trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#_propose,Method trunk.BIP.Bayes.Samplers.MCMC._Sampler._propose()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_propose"><a title="trunk.BIP.Bayes.Samplers.MCMC.Metropolis._propose
trunk.BIP.Bayes.Samplers.MCMC._Sampler._propose" class="py-name" href="#" onclick="return doclink('link-105', '_propose', 'link-105');">_propose</a></tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-106', 'po', 'link-70');">po</a></tt><tt class="py-op">)</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line">            <tt class="py-comment">#calculate likelihoods</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line">            <tt class="py-name">lik</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld._output_loglike" class="py-name" href="#" onclick="return doclink('link-107', '_output_loglike', 'link-15');">_output_loglike</a></tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likfun</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-108', 'po', 'link-70');">po</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">prop</tt><tt class="py-op">]</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line"> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line"><tt class="py-comment">#            print "lik:" , lik,  last_lik,  j</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line">            <tt class="py-name">accepted</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler._accept()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_accept"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._accept" class="py-name" href="#" onclick="return doclink('link-109', '_accept', 'link-109');">_accept</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">last_lik</tt><tt class="py-op">,</tt> <tt class="py-name">lik</tt><tt class="py-op">)</tt><tt class="py-comment"># have to include self in the call because method is vectorized.</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line"><tt class="py-comment">#            print "acc:", accepted,  theta</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt>  <tt class="py-line">            <tt class="py-comment">#Decide whether to accept proposal</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">last_lik</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-comment">#on first sample</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line">                <tt class="py-name">last_lik</tt> <tt class="py-op">=</tt> <tt class="py-name">lik</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">+=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">accepted</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">:</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line">                <tt class="py-name">rej</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">-</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">accepted</tt><tt class="py-op">)</tt> <tt class="py-comment">#adjust rejection counter</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt>  </tt>
<a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line">                    <tt class="py-name">ar</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-name">rej</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler._tune_likvar()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_tune_likvar"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._tune_likvar" class="py-name" href="#" onclick="return doclink('link-110', '_tune_likvar', 'link-110');">_tune_likvar</a></tt><tt class="py-op">(</tt><tt class="py-name">ar</tt><tt class="py-op">)</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance" class="py-name" href="#" onclick="return doclink('link-111', 'trace_acceptance', 'link-4');">trace_acceptance</a></tt><tt class="py-op">:</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-string">"--&gt; %s: Acc. ratio: %s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">rej</tt><tt class="py-op">,</tt> <tt class="py-name">ar</tt><tt class="py-op">)</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line">            <tt class="py-comment"># Store accepted values</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line"><tt class="py-comment">#            print "nchains:", self.nchains</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">c</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">pr</tt><tt class="py-op">,</tt>  <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">theta</tt><tt class="py-op">,</tt> <tt class="py-name">prop</tt><tt class="py-op">,</tt> <tt class="py-name">accepted</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#Iterates over the results of each chain</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line">                <tt class="py-comment">#if not accepted repeat last value</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">a</tt><tt class="py-op">:</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">history</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">t</tt>  </tt>
<a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-112', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt>  <tt class="py-line">                <tt class="py-comment">#self.seqhist[c, :, j] = t </tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">pr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">else</tt> <tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">point</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">point</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pr</tt><tt class="py-op">]</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line">                <tt class="py-name">ptheta</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-113', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">j</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt><tt class="py-keyword">break</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line">                <tt class="py-name">j</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> <tt class="py-comment">#update accepted sample counter </tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line">            <tt class="py-comment">#print j,  len(self.seqhist[0])</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">j</tt><tt class="py-op">%</tt><tt class="py-number">100</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">j</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance" class="py-name" href="#" onclick="return doclink('link-114', 'trace_acceptance', 'link-4');">trace_acceptance</a></tt><tt class="py-op">:</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt>  <tt class="py-line">                    <tt class="py-keyword">print</tt> <tt class="py-string">"++&gt;%s,%s: Acc. ratio: %s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">ar</tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler._watch_chain()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#_watch_chain"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._watch_chain" class="py-name" href="#" onclick="return doclink('link-115', '_watch_chain', 'link-115');">_watch_chain</a></tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_convergence" class="py-name" href="#" onclick="return doclink('link-116', 'trace_convergence', 'link-5');">trace_convergence</a></tt><tt class="py-op">:</tt> <tt class="py-keyword">print</tt> <tt class="py-string">"++&gt; %s: Likvar: %s\nML:%s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-117', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt>  <tt class="py-line"><tt class="py-comment">#            print "%s\r"%j</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt>  <tt class="py-line">            <tt class="py-name">last_lik</tt> <tt class="py-op">=</tt> <tt class="py-name">lik</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt>  <tt class="py-line">            <tt class="py-name">last_prop</tt> <tt class="py-op">=</tt> <tt class="py-name">prop</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line">            <tt class="py-name">last_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">theta</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line">            <tt class="py-name">ar</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-name">rej</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt> <tt class="py-op">==</tt><tt class="py-number">2</tt> <tt class="py-keyword">and</tt> <tt class="py-name">j</tt><tt class="py-op">&gt;</tt><tt class="py-number">10</tt><tt class="py-op">:</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name" targets="Method trunk.BIP.Bayes.Melding.Meld.current_plot()=trunk.BIP.Bayes.Melding.Meld-class.html#current_plot"><a title="trunk.BIP.Bayes.Melding.Meld.current_plot" class="py-name" href="#" onclick="return doclink('link-118', 'current_plot', 'link-118');">current_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.best_prop_index()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#best_prop_index"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.best_prop_index" class="py-name" href="#" onclick="return doclink('link-119', 'best_prop_index', 'link-119');">best_prop_index</a></tt><tt class="py-op">,</tt> <tt id="link-120" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-120', 'step', 'link-59');">step</a></tt><tt class="py-op">=</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.term_pool" class="py-name" href="#" onclick="return doclink('link-121', 'term_pool', 'link-26');">term_pool</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">ptheta</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">ptheta</tt><tt class="py-comment">#self._imp_sample(self.meld.L,ptheta,liklist)</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">likmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-122', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">)</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-123', 'DIC', 'link-16');">DIC</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-124', 'DIC', 'link-16');">DIC</a></tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Total steps(i): "</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-string">"rej:"</tt><tt class="py-op">,</tt><tt class="py-name">rej</tt><tt class="py-op">,</tt> <tt class="py-string">"j:"</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"&gt;&gt;&gt; Acceptance rate: %s"</tt><tt class="py-op">%</tt><tt class="py-name">ar</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.shut_down" class="py-name" href="#" onclick="return doclink('link-125', 'shut_down', 'link-104');">shut_down</a></tt><tt class="py-op">(</tt><tt class="py-string">'Finished normally'</tt><tt class="py-op">)</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L500"></a><tt class="py-lineno">500</tt>  <tt class="py-line"> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt>  <tt class="py-line"> </tt>
<a name="Metropolis._rms_fit"></a><div id="Metropolis._rms_fit-def"><a name="L502"></a><tt class="py-lineno">502</tt> <a class="py-toggle" href="#" id="Metropolis._rms_fit-toggle" onclick="return toggle('Metropolis._rms_fit');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#_rms_fit">_rms_fit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s1</tt><tt class="py-op">,</tt> <tt class="py-param">s2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Metropolis._rms_fit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Metropolis._rms_fit-expanded"><a name="L503"></a><tt class="py-lineno">503</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt>  <tt class="py-line"><tt class="py-docstring">        Calculates a basic fitness calculation between a model-</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt>  <tt class="py-line"><tt class="py-docstring">        generated time series and a observed time series.</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt>  <tt class="py-line"><tt class="py-docstring">        It uses a normalized RMS variation.</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt>  <tt class="py-line"><tt class="py-docstring">            - `s1`: model-generated time series. </tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt>  <tt class="py-line"><tt class="py-docstring">            - `s2`: observed time series. dictionary with keys matching names of s1</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt>  <tt class="py-line"><tt class="py-docstring">        :Types:</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt>  <tt class="py-line"><tt class="py-docstring">            - `s1`: Record array or list.</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt>  <tt class="py-line"><tt class="py-docstring">            - `s2`: Dictionary or list</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt>  <tt class="py-line"><tt class="py-docstring">        s1 and s2 can also be both lists of lists or lists of arrays of the same length.</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt>  <tt class="py-line"><tt class="py-docstring">        :Return:</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt>  <tt class="py-line"><tt class="py-docstring">            Inverse of the Root mean square deviation between `s1` and `s2`.</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">recarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt>  <tt class="py-line">            <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt>  <tt class="py-line">            <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">s2</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt>  <tt class="py-line">                <tt id="link-126" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-126', 'e', 'link-8');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">s2</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2.</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt>  <tt class="py-line">                <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-127', 'e', 'link-8');">e</a></tt><tt class="py-op">)</tt>  </tt>
<a name="L526"></a><tt class="py-lineno">526</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt>  <tt class="py-line">            <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">,</tt> <tt class="py-name">list</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt>  <tt class="py-line">            <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">-</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2.</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">s1</tt><tt class="py-op">,</tt> <tt class="py-name">s2</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt>  <tt class="py-line">        <tt class="py-name">rmsd</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt>  <tt class="py-line">        <tt class="py-name">fit</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">rmsd</tt> <tt class="py-comment">#fitness measure</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt>  <tt class="py-line"><tt class="py-comment">#        print "rmsd, fit, err: ", rmsd,fit, err</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">fit</tt> <tt class="py-op">==</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt><tt class="py-op">:</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt>  <tt class="py-line">            <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">fit</tt> <tt class="py-comment">#mean r-squared</tt> </tt>
</div><a name="L535"></a><tt class="py-lineno">535</tt>  <tt class="py-line"> </tt>
<a name="Metropolis._imp_sample"></a><div id="Metropolis._imp_sample-def"><a name="L536"></a><tt class="py-lineno">536</tt> <a class="py-toggle" href="#" id="Metropolis._imp_sample-toggle" onclick="return toggle('Metropolis._imp_sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#_imp_sample">_imp_sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">n</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">w</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Metropolis._imp_sample-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Metropolis._imp_sample-expanded"><a name="L537"></a><tt class="py-lineno">537</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt>  <tt class="py-line"><tt class="py-docstring">        Importance sampling</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt>  <tt class="py-line"><tt class="py-docstring">            - `n`: Number of samples to return</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: record array (containing on or more vectors of data) to be resampled</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt>  <tt class="py-line"><tt class="py-docstring">            - `w`: Weight vector</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt>  <tt class="py-line"><tt class="py-docstring">            returns a sample of size n</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt>  <tt class="py-line">        <tt class="py-comment">#sanitizing weights</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Starting importance Sampling"</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">/=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt>  <tt class="py-line">        <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">nan_to_num</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt>  <tt class="py-line">        <tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt>  <tt class="py-line">        <tt class="py-name">k</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt>  <tt class="py-line">        <tt class="py-name">nvar</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt>  <tt class="py-line">        <tt class="py-name">smp</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">descr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nvar</tt><tt class="py-op">,</tt><tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt>  <tt class="py-line">        <tt class="py-comment">#smp = copy.deepcopy(data[:n])</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">size</tt><tt class="py-op">)</tt><tt class="py-comment"># Random position of w</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt>  <tt class="py-line">                <tt class="py-name">smp</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt>  <tt class="py-line">                <tt class="py-name">j</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt>  <tt class="py-line">            <tt class="py-name">k</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Done importance sampling."</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">smp</tt> </tt>
</div><a name="L564"></a><tt class="py-lineno">564</tt>  <tt class="py-line"> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt>  <tt class="py-line"><tt class="py-comment">#    def _watch_chain(self, j):</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt>  <tt class="py-line"><tt class="py-comment">#        if j&lt;100:</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt>  <tt class="py-line"><tt class="py-comment">#            return</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt>  <tt class="py-line"><tt class="py-comment">#        self.gr_convergence(j, j-100)</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt>  <tt class="py-line"><tt class="py-comment">#        self.pserver.clearFig()</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt>  <tt class="py-line"><tt class="py-comment">#        thin = j//500 if j//500 !=0 else 1 #history is thinned to show at most 500 points, equally spaced over the entire range</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt>  <tt class="py-line"><tt class="py-comment">#        data = self.history[:j:thin].T.tolist()</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt>  <tt class="py-line"><tt class="py-comment">#        self.pserver.plotlines(data,range(j-(len(data[0])), j), self.parnames, "Chain Progress. GR Convergence: %s"%self._R,'points' , 1) </tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt>  <tt class="py-line"> </tt>
<a name="Metropolis._add_salt"></a><div id="Metropolis._add_salt-def"><a name="L574"></a><tt class="py-lineno">574</tt> <a class="py-toggle" href="#" id="Metropolis._add_salt-toggle" onclick="return toggle('Metropolis._add_salt');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#_add_salt">_add_salt</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">dataset</tt><tt class="py-op">,</tt><tt class="py-param">band</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Metropolis._add_salt-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Metropolis._add_salt-expanded"><a name="L575"></a><tt class="py-lineno">575</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt>  <tt class="py-line"><tt class="py-docstring">        Adds a few extra uniformly distributed data </tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt>  <tt class="py-line"><tt class="py-docstring">        points beyond the dataset range.</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt>  <tt class="py-line"><tt class="py-docstring">        This is done by adding from a uniform dist.</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt>  <tt class="py-line"><tt class="py-docstring">            - `dataset`: vector of data</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt>  <tt class="py-line"><tt class="py-docstring">            - `band`: Fraction of range to extend: [0,1[</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt>  <tt class="py-line"><tt class="py-docstring">            Salted dataset.</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt>  <tt class="py-line">        <tt class="py-name">dmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">)</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt>  <tt class="py-line">        <tt class="py-name">dmin</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">)</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt>  <tt class="py-line">        <tt class="py-name">drange</tt> <tt class="py-op">=</tt> <tt class="py-name">dmax</tt><tt class="py-op">-</tt><tt class="py-name">dmin</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt>  <tt class="py-line">        <tt class="py-name">hb</tt> <tt class="py-op">=</tt> <tt class="py-name">drange</tt><tt class="py-op">*</tt><tt class="py-name">band</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt>  <tt class="py-line">        <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">concatenate</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">dataset</tt><tt class="py-op">,</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">(</tt><tt class="py-name">dmin</tt><tt class="py-op">-</tt><tt class="py-name">hb</tt><tt class="py-op">,</tt><tt class="py-name">dmax</tt><tt class="py-op">-</tt><tt class="py-name">dmin</tt><tt class="py-op">+</tt><tt class="py-name">hb</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">K</tt><tt class="py-op">*</tt><tt class="py-number">.05</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">d</tt> </tt>
</div></div><a name="L592"></a><tt class="py-lineno">592</tt>  <tt class="py-line"> </tt>
<a name="model_as_ra"></a><div id="model_as_ra-def"><a name="L593"></a><tt class="py-lineno">593</tt>  <tt class="py-line"> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <a class="py-toggle" href="#" id="model_as_ra-toggle" onclick="return toggle('model_as_ra');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC-module.html#model_as_ra">model_as_ra</a><tt class="py-op">(</tt><tt class="py-param">theta</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">phinames</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="model_as_ra-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="model_as_ra-expanded"><a name="L595"></a><tt class="py-lineno">595</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt>  <tt class="py-line"><tt class="py-docstring">    Does a single run of self.model and returns the results as a record array</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt>  <tt class="py-line">    <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt>  <tt class="py-line">    <tt class="py-name">nphi</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">phinames</tt><tt class="py-op">)</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt>  <tt class="py-line">    <tt id="link-128" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-128', 'r', 'link-56');">r</a></tt> <tt class="py-op">=</tt> <tt id="link-129" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-129', 'model', 'link-73');">model</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt>  <tt class="py-line">    <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt id="link-130" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-130', 'r', 'link-56');">r</a></tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">phinames</tt><tt class="py-op">)</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt>  <tt class="py-line">        <tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-131" class="py-name"><a title="trunk.BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-131', 'r', 'link-56');">r</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L605"></a><tt class="py-lineno">605</tt>  <tt class="py-line"> </tt>
<a name="Dream"></a><div id="Dream-def"><a name="L606"></a><tt class="py-lineno">606</tt> <a class="py-toggle" href="#" id="Dream-toggle" onclick="return toggle('Dream');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html">Dream</a><tt class="py-op">(</tt><tt class="py-base-class">_Sampler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Dream-expanded"><a name="L607"></a><tt class="py-lineno">607</tt>  <tt class="py-line">    <tt class="py-docstring">'''</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt>  <tt class="py-line"><tt class="py-docstring">    DiffeRential Evolution Adaptive Markov chain sampler</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="Dream.__init__"></a><div id="Dream.__init__-def"><a name="L610"></a><tt class="py-lineno">610</tt> <a class="py-toggle" href="#" id="Dream.__init__-toggle" onclick="return toggle('Dream.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">meldobj</tt><tt class="py-op">,</tt> <tt class="py-param">samples</tt><tt class="py-op">,</tt> <tt class="py-param">sampmax</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt> <tt class="py-op">,</tt> <tt class="py-param">parpriors</tt><tt class="py-op">,</tt> <tt class="py-param">parnames</tt><tt class="py-op">,</tt> <tt class="py-param">parlimits</tt><tt class="py-op">,</tt><tt class="py-param">likfun</tt><tt class="py-op">,</tt> <tt class="py-param">likvariance</tt><tt class="py-op">,</tt> <tt class="py-param">burnin</tt><tt class="py-op">,</tt> <tt class="py-param">thin</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-param">convergenceCriteria</tt> <tt class="py-op">=</tt> <tt class="py-number">1.1</tt><tt class="py-op">,</tt>  <tt class="py-param">nCR</tt> <tt class="py-op">=</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-param">DEpairs</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">adaptationRate</tt> <tt class="py-op">=</tt> <tt class="py-number">.65</tt><tt class="py-op">,</tt> <tt class="py-param">eps</tt> <tt class="py-op">=</tt> <tt class="py-number">5e-6</tt><tt class="py-op">,</tt> <tt class="py-param">mConvergence</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">mAccept</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream.__init__-expanded"><a name="L611"></a><tt class="py-lineno">611</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt> <tt class="py-op">=</tt> <tt class="py-name">meldobj</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt> <tt class="py-op">=</tt> <tt class="py-name">samples</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sampmax</tt> <tt class="py-op">=</tt> <tt class="py-name">sampmax</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">t</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt> <tt class="py-op">=</tt> <tt class="py-name">parpriors</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt> <tt class="py-op">=</tt> <tt class="py-name">parnames</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt> <tt class="py-op">=</tt> <tt class="py-name">parlimits</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likfun</tt> <tt class="py-op">=</tt> <tt class="py-name">likfun</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt> <tt class="py-op">=</tt> <tt class="py-name">likvariance</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt> <tt class="py-op">=</tt> <tt class="py-name">burnin</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">parpriors</tt><tt class="py-op">)</tt>  </tt>
<a name="L623"></a><tt class="py-lineno">623</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">,</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">nphi</tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nCR</tt> <tt class="py-op">=</tt> <tt class="py-name">nCR</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">DEpairs</tt> <tt class="py-op">=</tt> <tt class="py-name">DEpairs</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">delayRej</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">kwargs</tt><tt class="py-op">:</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwargs</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt>  <tt class="py-line">                <tt class="py-keyword">exec</tt><tt class="py-op">(</tt><tt class="py-string">'self.%s = %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._R" class="py-name" href="#" onclick="return doclink('link-132', '_R', 'link-10');">_R</a></tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt> <tt class="py-comment">#initializing _R</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">maxChainDraws</tt> <tt class="py-op">=</tt> <tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">samples</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt>  <tt class="py-line">        <tt class="py-comment">#initialize the history arrays</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt>  <tt class="py-line">        <tt class="py-comment"># History of log posterior probs for all chains</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">omega</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt>  <tt class="py-line">        <tt class="py-comment"># Combined history of accepted samples</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">history</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-133', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-134', 'seqhist', 'link-6');">seqhist</a></tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt>  <tt class="py-line">        <tt class="py-comment">#self.sequenceHistories = np.zeros((self.nchains, self.dimensions, self.maxChainDraws))</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt>  <tt class="py-line">        <tt class="py-comment"># initialize the temporary storage vectors</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentVectors</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-135', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentLiks</tt> <tt class="py-op">=</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">-</tt><tt class="py-name">inf</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt> <tt class="py-op">=</tt> <tt class="py-number">2.38</tt><tt class="py-op">/</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">DEpairs</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-136', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.setup_xmlrpc_plotserver" class="py-name" href="#" onclick="return doclink('link-137', 'setup_xmlrpc_plotserver', 'link-80');">setup_xmlrpc_plotserver</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L644"></a><tt class="py-lineno">644</tt>  <tt class="py-line"> </tt>
<a name="Dream._det_outlier_chains"></a><div id="Dream._det_outlier_chains-def"><a name="L645"></a><tt class="py-lineno">645</tt> <a class="py-toggle" href="#" id="Dream._det_outlier_chains-toggle" onclick="return toggle('Dream._det_outlier_chains');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_det_outlier_chains">_det_outlier_chains</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">step</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream._det_outlier_chains-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream._det_outlier_chains-expanded"><a name="L646"></a><tt class="py-lineno">646</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt>  <tt class="py-line"><tt class="py-docstring">        Determine which chains are outliers</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt>  <tt class="py-line">        <tt class="py-name">means</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">omega</tt><tt class="py-op">[</tt><tt id="link-138" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-138', 'step', 'link-59');">step</a></tt><tt class="py-op">//</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt id="link-139" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-139', 'step', 'link-59');">step</a></tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt>  <tt class="py-line">        <tt class="py-name">q1</tt> <tt class="py-op">=</tt> <tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">omega</tt><tt class="py-op">[</tt><tt id="link-140" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-140', 'step', 'link-59');">step</a></tt><tt class="py-op">//</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt id="link-141" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-141', 'step', 'link-59');">step</a></tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">25</tt><tt class="py-op">)</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt>  <tt class="py-line">        <tt class="py-name">q3</tt> <tt class="py-op">=</tt> <tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">omega</tt><tt class="py-op">[</tt><tt id="link-142" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-142', 'step', 'link-59');">step</a></tt><tt class="py-op">//</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt id="link-143" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-143', 'step', 'link-59');">step</a></tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">75</tt><tt class="py-op">)</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt>  <tt class="py-line">        <tt class="py-name">iqr</tt> <tt class="py-op">=</tt> <tt class="py-name">q3</tt><tt class="py-op">-</tt><tt class="py-name">q1</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt>  <tt class="py-line">        <tt class="py-name">outl</tt> <tt class="py-op">=</tt> <tt class="py-name">means</tt><tt class="py-op">&lt;</tt><tt class="py-name">q1</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">iqr</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">outl</tt> </tt>
</div><a name="L655"></a><tt class="py-lineno">655</tt>  <tt class="py-line"><tt class="py-comment">#    @timeit</tt> </tt>
<a name="Dream.delayed_rejection"></a><div id="Dream.delayed_rejection-def"><a name="L656"></a><tt class="py-lineno">656</tt> <a class="py-toggle" href="#" id="Dream.delayed_rejection-toggle" onclick="return toggle('Dream.delayed_rejection');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#delayed_rejection">delayed_rejection</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">xi</tt><tt class="py-op">,</tt> <tt class="py-param">zi</tt><tt class="py-op">,</tt> <tt class="py-param">pxi</tt><tt class="py-op">,</tt> <tt class="py-param">zprob</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream.delayed_rejection-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream.delayed_rejection-expanded"><a name="L657"></a><tt class="py-lineno">657</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt>  <tt class="py-line"><tt class="py-docstring">        Generates a second proposal based on rejected proposal xi</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt>  <tt class="py-line">        <tt class="py-name">k</tt><tt class="py-op">=</tt><tt class="py-number">.3</tt> <tt class="py-comment">#Deflation factor for the second proposal</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt>  <tt class="py-line">        <tt class="py-name">cv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt><tt class="py-op">*</tt><tt class="py-name">cov</tt><tt class="py-op">(</tt><tt class="py-name">xi</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scaling_factor</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-144', 'e', 'link-8');">e</a></tt><tt class="py-op">*</tt><tt class="py-name">identity</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-145', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt>  <tt class="py-line">        <tt class="py-name">o</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">o</tt><tt class="py-op">&lt;</tt><tt class="py-number">50</tt><tt class="py-op">:</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt>  <tt class="py-line">            <tt class="py-name">zdr</tt> <tt class="py-op">=</tt> <tt class="py-name">multivariate_normal</tt><tt class="py-op">(</tt><tt class="py-name">xi</tt><tt class="py-op">,</tt><tt class="py-name">k</tt><tt class="py-op">*</tt><tt class="py-name">cv</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.check_constraints" class="py-name" href="#" onclick="return doclink('link-146', 'check_constraints', 'link-61');">check_constraints</a></tt><tt class="py-op">(</tt><tt class="py-name">zdr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">continue</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">t</tt><tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">t</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">zdr</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-147', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">:</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt>  <tt class="py-line">            <tt class="py-name">o</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sum</tt> <tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">t</tt><tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">t</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">zdr</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-148', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">:</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">xi</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt>  <tt class="py-line">        <tt class="py-name">propphi_zdr</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream._prop_phi()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_prop_phi"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._prop_phi" class="py-name" href="#" onclick="return doclink('link-149', '_prop_phi', 'link-149');">_prop_phi</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">zdr</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt>  <tt class="py-line"><tt class="py-comment">#        print propphi_zdr, zdr</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt>  <tt class="py-line">        <tt class="py-name">zdrprob</tt><tt class="py-op">,</tt>  <tt class="py-name">zdrlik</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream._get_post_prob()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_get_post_prob"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._get_post_prob" class="py-name" href="#" onclick="return doclink('link-150', '_get_post_prob', 'link-150');">_get_post_prob</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">zdr</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">propphi_zdr</tt><tt class="py-op">)</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt>  <tt class="py-line">        <tt class="py-name">alpha2</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">zdrprob</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream._alpha1()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_alpha1"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._alpha1" class="py-name" href="#" onclick="return doclink('link-151', '_alpha1', 'link-151');">_alpha1</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">zdrprob</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">zprob</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">pxi</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._alpha1" class="py-name" href="#" onclick="return doclink('link-152', '_alpha1', 'link-151');">_alpha1</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">pxi</tt><tt class="py-op">,</tt> <tt class="py-name">zprob</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt>  <tt class="py-line">        <tt class="py-name">acc</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt> <tt class="py-name">lik</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt> <tt class="py-name">pr</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt> <tt class="py-name">prop</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt> <tt class="py-name">alpha2</tt><tt class="py-op">:</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt>  <tt class="py-line">            <tt class="py-name">xi</tt> <tt class="py-op">=</tt> <tt class="py-name">zdr</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt>  <tt class="py-line">            <tt class="py-name">acc</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt>  <tt class="py-line">            <tt class="py-name">liks</tt> <tt class="py-op">=</tt> <tt class="py-name">zdrlik</tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt>  <tt class="py-line">            <tt class="py-name">pr</tt> <tt class="py-op">=</tt> <tt class="py-name">zdrprob</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt>  <tt class="py-line">            <tt class="py-name">prop</tt> <tt class="py-op">=</tt> <tt class="py-name">propphi_zdr</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">xi</tt><tt class="py-op">,</tt> <tt class="py-name">acc</tt><tt class="py-op">,</tt> <tt class="py-name">lik</tt><tt class="py-op">,</tt> <tt class="py-name">pr</tt><tt class="py-op">,</tt> <tt class="py-name">prop</tt> </tt>
</div><a name="L683"></a><tt class="py-lineno">683</tt>  <tt class="py-line"> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">np</tt><tt class="py-op">.</tt><tt class="py-name">vectorize</tt> </tt>
<a name="Dream._alpha1"></a><div id="Dream._alpha1-def"><a name="L685"></a><tt class="py-lineno">685</tt> <a class="py-toggle" href="#" id="Dream._alpha1-toggle" onclick="return toggle('Dream._alpha1');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_alpha1">_alpha1</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">p1</tt><tt class="py-op">,</tt> <tt class="py-param">p2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream._alpha1-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream._alpha1-expanded"><a name="L686"></a><tt class="py-lineno">686</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt>  <tt class="py-line"><tt class="py-docstring">        Returns the Metropolis acceptance probability:</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt>  <tt class="py-line"><tt class="py-docstring">        alpha1(p1,p1) = min(1,p1/p2) if p2 &gt;-np.inf else 1</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt>  <tt class="py-line"><tt class="py-docstring">            - `p1`: log probability</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt>  <tt class="py-line"><tt class="py-docstring">            - `p2`: log probability</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-153" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-153', 'p2', 'link-44');">p2</a></tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt id="link-154" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-154', 'p2', 'link-44');">p2</a></tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">inf</tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt>  <tt class="py-line">        <tt class="py-comment"># ps are log probabilities</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-155" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-155', 'p2', 'link-44');">p2</a></tt> <tt class="py-op">&gt;</tt><tt class="py-op">-</tt><tt class="py-name">inf</tt><tt class="py-op">:</tt><tt class="py-comment">#np.exp(p2)&gt;0</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt>  <tt class="py-line">            <tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt> <tt class="py-name">exp</tt><tt class="py-op">(</tt><tt id="link-156" class="py-name" targets="Function trunk.BIP.SDE.gillespie.p1()=trunk.BIP.SDE.gillespie-module.html#p1"><a title="trunk.BIP.SDE.gillespie.p1" class="py-name" href="#" onclick="return doclink('link-156', 'p1', 'link-156');">p1</a></tt><tt class="py-op">-</tt><tt id="link-157" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-157', 'p2', 'link-44');">p2</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt id="link-158" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-158', 'p2', 'link-44');">p2</a></tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-name">inf</tt><tt class="py-op">:</tt><tt class="py-comment">#np.exp(p2)==0</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt>  <tt class="py-line">            <tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"proposal's logP: "</tt><tt class="py-op">,</tt> <tt id="link-159" class="py-name"><a title="trunk.BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-159', 'p2', 'link-44');">p2</a></tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt>  <tt class="py-line">            <tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">alpha</tt> </tt>
</div><a name="L704"></a><tt class="py-lineno">704</tt>  <tt class="py-line">         </tt>
<a name="L705"></a><tt class="py-lineno">705</tt>  <tt class="py-line"> </tt>
<a name="Dream.update_CR_dist"></a><div id="Dream.update_CR_dist-def"><a name="L706"></a><tt class="py-lineno">706</tt> <a class="py-toggle" href="#" id="Dream.update_CR_dist-toggle" onclick="return toggle('Dream.update_CR_dist');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#update_CR_dist">update_CR_dist</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream.update_CR_dist-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream.update_CR_dist-expanded"><a name="L707"></a><tt class="py-lineno">707</tt>  <tt class="py-line">        <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt>  <tt class="py-line">        <tt class="py-name">Lm</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt>  </tt>
<a name="L709"></a><tt class="py-lineno">709</tt>  <tt class="py-line">        <tt class="py-name">pm</tt> <tt class="py-op">=</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nCR</tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt>  <tt class="py-line"> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt>  <tt class="py-line">            <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">multinomial</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">pm</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nCR</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">nonzero</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt>  <tt class="py-line">            <tt class="py-name">CR</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nCR</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt>  <tt class="py-line">            <tt class="py-name">Lm</tt> <tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
</div><a name="L715"></a><tt class="py-lineno">715</tt>  <tt class="py-line">            <tt class="py-comment">#TODO: finish implementing this</tt> </tt>
<a name="L716"></a><tt class="py-lineno">716</tt>  <tt class="py-line"> </tt>
<a name="Dream._prop_initial_theta"></a><div id="Dream._prop_initial_theta-def"><a name="L717"></a><tt class="py-lineno">717</tt> <a class="py-toggle" href="#" id="Dream._prop_initial_theta-toggle" onclick="return toggle('Dream._prop_initial_theta');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_prop_initial_theta">_prop_initial_theta</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">step</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream._prop_initial_theta-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream._prop_initial_theta-expanded"><a name="L718"></a><tt class="py-lineno">718</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt>  <tt class="py-line"><tt class="py-docstring">        Generate Theta proposals from priors</tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">initheta</tt><tt class="py-op">:</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt>  <tt class="py-line">            <tt class="py-comment">#start from user-defined point in parameter space.</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">initheta</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt>  <tt class="py-line">             </tt>
<a name="L725"></a><tt class="py-lineno">725</tt>  <tt class="py-line">        <tt class="py-name">thetalist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt>  <tt class="py-line">        <tt class="py-name">initcov</tt> <tt class="py-op">=</tt> <tt class="py-name">identity</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-160', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt>  <tt class="py-line">            <tt class="py-comment">#sample from the priors</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt>  <tt class="py-line"><tt class="py-comment">#            while 1:</tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt>  <tt class="py-line">            <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt><tt class="py-op">[</tt><tt class="py-name">par</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt><tt class="py-op">(</tt><tt class="py-name">moments</tt><tt class="py-op">=</tt><tt class="py-string">'m'</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">par</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L731"></a><tt class="py-lineno">731</tt>  <tt class="py-line"><tt class="py-comment">#                if sum ([int(t&gt;= self.parlimits[i][0] and t&lt;= self.parlimits[i][1]) for i, t in enumerate(theta)]) == self.dimensions:</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt>  <tt class="py-line"><tt class="py-comment">#                    break</tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lastcv</tt> <tt class="py-op">=</tt> <tt class="py-name">initcov</tt> <tt class="py-comment">#assume no covariance at the beginning</tt> </tt>
<a name="L734"></a><tt class="py-lineno">734</tt>  <tt class="py-line"> </tt>
<a name="L735"></a><tt class="py-lineno">735</tt>  <tt class="py-line">            <tt class="py-name">thetalist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L736"></a><tt class="py-lineno">736</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">thetalist</tt>  </tt>
</div><a name="L737"></a><tt class="py-lineno">737</tt>  <tt class="py-line">         </tt>
<a name="L738"></a><tt class="py-lineno">738</tt>  <tt class="py-line"><tt class="py-comment">#    @timeit</tt> </tt>
<a name="Dream._prop_phi"></a><div id="Dream._prop_phi-def"><a name="L739"></a><tt class="py-lineno">739</tt> <a class="py-toggle" href="#" id="Dream._prop_phi-toggle" onclick="return toggle('Dream._prop_phi');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_prop_phi">_prop_phi</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">thetalist</tt><tt class="py-op">,</tt> <tt class="py-param">po</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream._prop_phi-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream._prop_phi-expanded"><a name="L740"></a><tt class="py-lineno">740</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt>  <tt class="py-line"><tt class="py-docstring">        Returns proposed Phi derived from theta</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-161" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-161', 'po', 'link-70');">po</a></tt><tt class="py-op">:</tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt>  <tt class="py-line">            <tt class="py-name">propl</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-162" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-162', 'po', 'link-70');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt id="link-163" class="py-name"><a title="trunk.BIP.Bayes.Melding.model_as_ra
trunk.BIP.Bayes.Samplers.MCMC.model_as_ra" class="py-name" href="#" onclick="return doclink('link-163', 'model_as_ra', 'link-72');">model_as_ra</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-164', 'model', 'link-73');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">thetalist</tt><tt class="py-op">]</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt>  <tt class="py-line">            <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">job</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt><tt class="py-op">]</tt>  <tt class="py-keyword">for</tt> <tt class="py-name">job</tt> <tt class="py-keyword">in</tt> <tt class="py-name">propl</tt><tt class="py-op">]</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt>  <tt class="py-line">            <tt class="py-name">proplist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-165" class="py-name"><a title="trunk.BIP.Bayes.Melding.model_as_ra
trunk.BIP.Bayes.Samplers.MCMC.model_as_ra" class="py-name" href="#" onclick="return doclink('link-165', 'model_as_ra', 'link-72');">model_as_ra</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-166', 'model', 'link-73');">model</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">thetalist</tt><tt class="py-op">]</tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">proplist</tt> </tt>
</div><a name="L749"></a><tt class="py-lineno">749</tt>  <tt class="py-line">         </tt>
<a name="L750"></a><tt class="py-lineno">750</tt>  <tt class="py-line"><tt class="py-comment">#    @timeit</tt> </tt>
<a name="Dream._chain_evolution"></a><div id="Dream._chain_evolution-def"><a name="L751"></a><tt class="py-lineno">751</tt> <a class="py-toggle" href="#" id="Dream._chain_evolution-toggle" onclick="return toggle('Dream._chain_evolution');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_chain_evolution">_chain_evolution</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">proptheta</tt><tt class="py-op">,</tt>  <tt class="py-param">propphi</tt><tt class="py-op">,</tt> <tt class="py-param">pps</tt><tt class="py-op">,</tt> <tt class="py-param">liks</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream._chain_evolution-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream._chain_evolution-expanded"><a name="L752"></a><tt class="py-lineno">752</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt>  <tt class="py-line"><tt class="py-docstring">        Chain evolution as describe in ter Braak's Dream algorithm.</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt>  <tt class="py-line">        <tt class="py-name">CR</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nCR</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt>  <tt class="py-line">        <tt class="py-name">b</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">10.</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">]</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt>  <tt class="py-line">        <tt class="py-name">delta</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">//</tt><tt class="py-number">2</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt> <tt class="py-op">&gt;</tt><tt class="py-number">2</tt> <tt class="py-keyword">else</tt> <tt class="py-number">1</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt>  <tt class="py-line">        <tt class="py-name">gam</tt> <tt class="py-op">=</tt> <tt class="py-number">2.38</tt><tt class="py-op">/</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">delta</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-167', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L759"></a><tt class="py-lineno">759</tt>  <tt class="py-line">        <tt class="py-name">zis</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L760"></a><tt class="py-lineno">760</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt>  <tt class="py-line">            <tt class="py-name">o</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-comment">#check constraints</tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt>  <tt class="py-line">                <tt id="link-168" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-168', 'e', 'link-8');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">uniform</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">b</tt><tt class="py-op">]</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt>  <tt class="py-line">                <tt class="py-name">eps</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">norm</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">b</tt><tt class="py-op">]</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt>  <tt class="py-line">                <tt class="py-name">others</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">proptheta</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-op">!=</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt>  <tt class="py-line">                <tt class="py-name">dif</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-169', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">delta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt>  <tt class="py-line">                    <tt class="py-name">d1</tt><tt class="py-op">,</tt> <tt class="py-name">d2</tt> <tt class="py-op">=</tt> <tt class="py-name">sample</tt><tt class="py-op">(</tt><tt class="py-name">others</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt>  <tt class="py-line">                    <tt class="py-name">dif</tt><tt class="py-op">+=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">d1</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">d2</tt><tt class="py-op">)</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt>  <tt class="py-line">                <tt class="py-name">zi</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">proptheta</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-170', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt id="link-171" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.e" class="py-name" href="#" onclick="return doclink('link-171', 'e', 'link-8');">e</a></tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">gam</tt><tt class="py-op">*</tt><tt class="py-name">dif</tt><tt class="py-op">+</tt><tt class="py-name">eps</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt>  <tt class="py-line">                <tt class="py-comment">#revert offlimits proposals</tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">zi</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">zi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">&lt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">or</tt> <tt class="py-name">zi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parlimits</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt><tt class="py-comment"># or isnan(zi):</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt>  <tt class="py-line">                        <tt class="py-name">zi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">proptheta</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt>  <tt class="py-line">                <tt class="py-comment">#Cross over</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">zi</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  </tt>
<a name="L777"></a><tt class="py-lineno">777</tt>  <tt class="py-line">                    <tt class="py-name">zi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">proptheta</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">rand</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">CR</tt> <tt class="py-keyword">else</tt> <tt class="py-name">zi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt>  <tt class="py-line">                <tt class="py-name">zis</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">zi</tt><tt class="py-op">)</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.check_constraints" class="py-name" href="#" onclick="return doclink('link-172', 'check_constraints', 'link-61');">check_constraints</a></tt><tt class="py-op">(</tt><tt class="py-name">zi</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  </tt>
<a name="L780"></a><tt class="py-lineno">780</tt>  <tt class="py-line">                    <tt class="py-keyword">break</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt>  <tt class="py-line">             </tt>
<a name="L782"></a><tt class="py-lineno">782</tt>  <tt class="py-line">        <tt class="py-comment">#get the associated Phi's</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt class="py-name">zis</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt>  <tt class="py-line">            <tt class="py-name">pdb</tt><tt class="py-op">.</tt><tt class="py-name">set_trace</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt>  <tt class="py-line">        <tt class="py-name">propphi_z</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._prop_phi" class="py-name" href="#" onclick="return doclink('link-173', '_prop_phi', 'link-149');">_prop_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">zis</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-174', 'po', 'link-70');">po</a></tt><tt class="py-op">)</tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt>  <tt class="py-line">        <tt class="py-name">zprobs</tt><tt class="py-op">,</tt>  <tt class="py-name">zliks</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._get_post_prob" class="py-name" href="#" onclick="return doclink('link-175', '_get_post_prob', 'link-150');">_get_post_prob</a></tt><tt class="py-op">(</tt><tt class="py-name">zis</tt><tt class="py-op">,</tt> <tt class="py-name">propphi_z</tt><tt class="py-op">)</tt> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt>  <tt class="py-line">        <tt class="py-name">prop_evo</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-176', 'dimensions', 'link-58');">dimensions</a></tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt>  <tt class="py-line">        <tt class="py-name">liks_evo</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-177', 'dimensions', 'link-58');">dimensions</a></tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt>  <tt class="py-line">         </tt>
<a name="L790"></a><tt class="py-lineno">790</tt>  <tt class="py-line">        <tt class="py-name">evolved</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-178', 'dimensions', 'link-58');">dimensions</a></tt> <tt class="py-comment">#evolved Theta</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt>  <tt class="py-line">        <tt class="py-name">prop_evo</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt>  <tt class="py-line">        <tt class="py-name">liks_evo</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-179', 'dimensions', 'link-58');">dimensions</a></tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt>  <tt class="py-line">        <tt class="py-name">pps_evo</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt> <tt class="py-comment">#posterior probabilities</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt>  <tt class="py-line">        <tt class="py-name">accepted</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._accept" class="py-name" href="#" onclick="return doclink('link-180', '_accept', 'link-109');">_accept</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">pps</tt><tt class="py-op">,</tt> <tt class="py-name">zprobs</tt><tt class="py-op">)</tt><tt class="py-comment">#have to pass self because method is vectorized</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt>  <tt class="py-line">         </tt>
<a name="L796"></a><tt class="py-lineno">796</tt>  <tt class="py-line">        <tt class="py-comment"># Do Delayed rejection with the chains that got rejected</tt> </tt>
<a name="L797"></a><tt class="py-lineno">797</tt>  <tt class="py-line">        <tt class="py-comment"># and store results.</tt> </tt>
<a name="L798"></a><tt class="py-lineno">798</tt>  <tt class="py-line">        <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">z</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">zis</tt><tt class="py-op">,</tt> <tt class="py-name">proptheta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">accepted</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt>  <tt class="py-line">                <tt class="py-name">evolved</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">z</tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt>  <tt class="py-line">                <tt class="py-name">prop_evo</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">propphi_z</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt>  <tt class="py-line">                <tt class="py-name">pps_evo</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">zprobs</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</tt>  <tt class="py-line">                <tt class="py-name">liks_evo</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">zliks</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L805"></a><tt class="py-lineno">805</tt>  <tt class="py-line">                <tt class="py-comment">#self.liklist.append(zliks[i])</tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt>  <tt class="py-line">                <tt class="py-name">th2</tt><tt class="py-op">,</tt><tt class="py-name">acc</tt><tt class="py-op">,</tt><tt class="py-name">lk</tt><tt class="py-op">,</tt><tt class="py-name">pr</tt><tt class="py-op">,</tt><tt class="py-name">prop</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream.delayed_rejection()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#delayed_rejection"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.delayed_rejection" class="py-name" href="#" onclick="return doclink('link-181', 'delayed_rejection', 'link-181');">delayed_rejection</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">,</tt><tt class="py-name">pps</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">zprobs</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">acc</tt><tt class="py-op">:</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt>  <tt class="py-line">                    <tt class="py-name">accepted</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L810"></a><tt class="py-lineno">810</tt>  <tt class="py-line">                    <tt class="py-comment">#self.liklist.append(lk)</tt> </tt>
<a name="L811"></a><tt class="py-lineno">811</tt>  <tt class="py-line">                <tt class="py-name">evolved</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">th2</tt> </tt>
<a name="L812"></a><tt class="py-lineno">812</tt>  <tt class="py-line">                <tt class="py-name">prop_evo</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">prop</tt> <tt class="py-keyword">if</tt> <tt class="py-name">acc</tt> <tt class="py-keyword">else</tt> <tt class="py-name">propphi</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L813"></a><tt class="py-lineno">813</tt>  <tt class="py-line">                <tt class="py-name">liks_evo</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lk</tt> <tt class="py-keyword">if</tt> <tt class="py-name">acc</tt> <tt class="py-keyword">else</tt> <tt class="py-name">liks</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L814"></a><tt class="py-lineno">814</tt>  <tt class="py-line">                <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L815"></a><tt class="py-lineno">815</tt>  <tt class="py-line">                    <tt class="py-name">pps_evo</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">pr</tt> <tt class="py-keyword">if</tt> <tt class="py-name">acc</tt> <tt class="py-keyword">else</tt> <tt class="py-name">pps</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L816"></a><tt class="py-lineno">816</tt>  <tt class="py-line">                <tt class="py-keyword">except</tt> <tt class="py-name">TypeError</tt><tt class="py-op">:</tt> <tt class="py-comment">#when pps == None</tt> </tt>
<a name="L817"></a><tt class="py-lineno">817</tt>  <tt class="py-line">                    <tt class="py-name">pps_evo</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">inf</tt> </tt>
<a name="L818"></a><tt class="py-lineno">818</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L819"></a><tt class="py-lineno">819</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">evolved</tt><tt class="py-op">,</tt> <tt class="py-name">prop_evo</tt><tt class="py-op">,</tt> <tt class="py-name">pps_evo</tt><tt class="py-op">,</tt> <tt class="py-name">liks_evo</tt><tt class="py-op">,</tt> <tt class="py-name">accepted</tt> </tt>
</div><a name="L820"></a><tt class="py-lineno">820</tt>  <tt class="py-line">         </tt>
<a name="L821"></a><tt class="py-lineno">821</tt>  <tt class="py-line"><tt class="py-comment">#    @timeit</tt> </tt>
<a name="Dream._get_post_prob"></a><div id="Dream._get_post_prob-def"><a name="L822"></a><tt class="py-lineno">822</tt> <a class="py-toggle" href="#" id="Dream._get_post_prob-toggle" onclick="return toggle('Dream._get_post_prob');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_get_post_prob">_get_post_prob</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">theta</tt><tt class="py-op">,</tt> <tt class="py-param">prop</tt><tt class="py-op">,</tt> <tt class="py-param">po</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream._get_post_prob-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream._get_post_prob-expanded"><a name="L823"></a><tt class="py-lineno">823</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L824"></a><tt class="py-lineno">824</tt>  <tt class="py-line"><tt class="py-docstring">        Calculates the posterior probability for the proposal of each chain</tt> </tt>
<a name="L825"></a><tt class="py-lineno">825</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L826"></a><tt class="py-lineno">826</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L827"></a><tt class="py-lineno">827</tt>  <tt class="py-line"><tt class="py-docstring">            - `theta`: list of nchains thetas</tt> </tt>
<a name="L828"></a><tt class="py-lineno">828</tt>  <tt class="py-line"><tt class="py-docstring">            - `prop`: list of nchains phis</tt> </tt>
<a name="L829"></a><tt class="py-lineno">829</tt>  <tt class="py-line"><tt class="py-docstring">            - `po`: Pool of processes</tt> </tt>
<a name="L830"></a><tt class="py-lineno">830</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L831"></a><tt class="py-lineno">831</tt>  <tt class="py-line"><tt class="py-docstring">        :Returns:</tt> </tt>
<a name="L832"></a><tt class="py-lineno">832</tt>  <tt class="py-line"><tt class="py-docstring">            - `posts`: list of log posterior probabilities of length self.nchains</tt> </tt>
<a name="L833"></a><tt class="py-lineno">833</tt>  <tt class="py-line"><tt class="py-docstring">            - `listoliks`: list of log-likelihoods of length self.nchains</tt> </tt>
<a name="L834"></a><tt class="py-lineno">834</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L835"></a><tt class="py-lineno">835</tt>  <tt class="py-line">        <tt class="py-name">pri</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L836"></a><tt class="py-lineno">836</tt>  <tt class="py-line">        <tt class="py-name">pris</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L837"></a><tt class="py-lineno">837</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-comment">#iterate over chains</tt> </tt>
<a name="L838"></a><tt class="py-lineno">838</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#iterate  over parameters</tt> </tt>
<a name="L839"></a><tt class="py-lineno">839</tt>  <tt class="py-line">                <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L840"></a><tt class="py-lineno">840</tt>  <tt class="py-line">                    <tt class="py-name">pri</tt> <tt class="py-op">*=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">pdf</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L841"></a><tt class="py-lineno">841</tt>  <tt class="py-line">                <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> <tt class="py-comment">#in case distribution is discrete</tt> </tt>
<a name="L842"></a><tt class="py-lineno">842</tt>  <tt class="py-line">                    <tt class="py-name">pri</tt> <tt class="py-op">*=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parpriors</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">pmf</tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L843"></a><tt class="py-lineno">843</tt>  <tt class="py-line">            <tt class="py-name">pris</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pri</tt><tt class="py-op">)</tt> </tt>
<a name="L844"></a><tt class="py-lineno">844</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-182" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-182', 'po', 'link-70');">po</a></tt><tt class="py-op">:</tt> </tt>
<a name="L845"></a><tt class="py-lineno">845</tt>  <tt class="py-line">            <tt class="py-name">listol</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-183" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-183', 'po', 'link-70');">po</a></tt><tt class="py-op">.</tt><tt class="py-name">apply_async</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld._output_loglike" class="py-name" href="#" onclick="return doclink('link-184', '_output_loglike', 'link-15');">_output_loglike</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likfun</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">prop</tt><tt class="py-op">]</tt> </tt>
<a name="L846"></a><tt class="py-lineno">846</tt>  <tt class="py-line">            <tt class="py-name">listoliks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">listol</tt><tt class="py-op">]</tt> </tt>
<a name="L847"></a><tt class="py-lineno">847</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-185" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.term_pool" class="py-name" href="#" onclick="return doclink('link-185', 'term_pool', 'link-26');">term_pool</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L848"></a><tt class="py-lineno">848</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L849"></a><tt class="py-lineno">849</tt>  <tt class="py-line">            <tt class="py-name">listoliks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld._output_loglike" class="py-name" href="#" onclick="return doclink('link-186', '_output_loglike', 'link-15');">_output_loglike</a></tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likfun</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">prop</tt><tt class="py-op">]</tt> </tt>
<a name="L850"></a><tt class="py-lineno">850</tt>  <tt class="py-line"><tt class="py-comment">#        Multiply by prior values to obtain posterior probs</tt> </tt>
<a name="L851"></a><tt class="py-lineno">851</tt>  <tt class="py-line"><tt class="py-comment">#        Actually sum the logs</tt> </tt>
<a name="L852"></a><tt class="py-lineno">852</tt>  <tt class="py-line">        <tt class="py-name">posts</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">pris</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">listoliks</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L853"></a><tt class="py-lineno">853</tt>  <tt class="py-line">         </tt>
<a name="L854"></a><tt class="py-lineno">854</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isnan</tt><tt class="py-op">(</tt><tt class="py-name">posts</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L855"></a><tt class="py-lineno">855</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">"\nLikelihoods returned some NaNs. Dropping to debug mode:\n"</tt> </tt>
<a name="L856"></a><tt class="py-lineno">856</tt>  <tt class="py-line">            <tt class="py-name">pdb</tt><tt class="py-op">.</tt><tt class="py-name">set_trace</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L857"></a><tt class="py-lineno">857</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">posts</tt><tt class="py-op">,</tt> <tt class="py-name">listoliks</tt> </tt>
</div><a name="L858"></a><tt class="py-lineno">858</tt>  <tt class="py-line">     </tt>
<a name="Dream.step"></a><div id="Dream.step-def"><a name="L859"></a><tt class="py-lineno">859</tt> <a class="py-toggle" href="#" id="Dream.step-toggle" onclick="return toggle('Dream.step');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#step">step</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dream.step-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dream.step-expanded"><a name="L860"></a><tt class="py-lineno">860</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L861"></a><tt class="py-lineno">861</tt>  <tt class="py-line"><tt class="py-docstring">        Does the actual sampling loop.</tt> </tt>
<a name="L862"></a><tt class="py-lineno">862</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L863"></a><tt class="py-lineno">863</tt>  <tt class="py-line">        <tt class="py-name">ptheta</tt> <tt class="py-op">=</tt> <tt class="py-name">recarray</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">,</tt><tt class="py-name">formats</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f8'</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.dimensions" class="py-name" href="#" onclick="return doclink('link-187', 'dimensions', 'link-58');">dimensions</a></tt><tt class="py-op">,</tt> <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parnames</tt><tt class="py-op">)</tt> </tt>
<a name="L864"></a><tt class="py-lineno">864</tt>  <tt class="py-line">        <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">j</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">rej</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt><tt class="py-name">ar</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment">#total samples,accepted samples, rejected proposals, acceptance rate</tt> </tt>
<a name="L865"></a><tt class="py-lineno">865</tt>  <tt class="py-line">        <tt class="py-name">last_pps</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L866"></a><tt class="py-lineno">866</tt>  <tt class="py-line">        <tt id="link-188" class="py-name" targets="Variable trunk.BIP.SDE.example.t0=trunk.BIP.SDE.example-module.html#t0"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-188', 't0', 'link-188');">t0</a></tt><tt class="py-op">=</tt><tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L867"></a><tt class="py-lineno">867</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt> </tt>
<a name="L868"></a><tt class="py-lineno">868</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">current_step</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt> </tt>
<a name="L869"></a><tt class="py-lineno">869</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">stop_now</tt><tt class="py-op">:</tt> </tt>
<a name="L870"></a><tt class="py-lineno">870</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.shut_down" class="py-name" href="#" onclick="return doclink('link-189', 'shut_down', 'link-104');">shut_down</a></tt><tt class="py-op">(</tt><tt class="py-string">'user interrupted'</tt><tt class="py-op">)</tt> </tt>
<a name="L871"></a><tt class="py-lineno">871</tt>  <tt class="py-line">            <tt class="py-comment">#generate proposals</tt> </tt>
<a name="L872"></a><tt class="py-lineno">872</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">j</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L873"></a><tt class="py-lineno">873</tt>  <tt class="py-line">                <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream._prop_initial_theta()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_prop_initial_theta"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._prop_initial_theta" class="py-name" href="#" onclick="return doclink('link-190', '_prop_initial_theta', 'link-190');">_prop_initial_theta</a></tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L874"></a><tt class="py-lineno">874</tt>  <tt class="py-line">                <tt class="py-name">prop</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._prop_phi" class="py-name" href="#" onclick="return doclink('link-191', '_prop_phi', 'link-149');">_prop_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-192', 'po', 'link-70');">po</a></tt><tt class="py-op">)</tt> </tt>
<a name="L875"></a><tt class="py-lineno">875</tt>  <tt class="py-line">                <tt class="py-name">pps</tt><tt class="py-op">,</tt> <tt class="py-name">liks</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._get_post_prob" class="py-name" href="#" onclick="return doclink('link-193', '_get_post_prob', 'link-150');">_get_post_prob</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt> <tt class="py-name">prop</tt><tt class="py-op">)</tt> </tt>
<a name="L876"></a><tt class="py-lineno">876</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L877"></a><tt class="py-lineno">877</tt>  <tt class="py-line">                <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-194', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L878"></a><tt class="py-lineno">878</tt>  <tt class="py-line">                <tt class="py-name">prop</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._prop_phi" class="py-name" href="#" onclick="return doclink('link-195', '_prop_phi', 'link-149');">_prop_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.po" class="py-name" href="#" onclick="return doclink('link-196', 'po', 'link-70');">po</a></tt><tt class="py-op">)</tt> </tt>
<a name="L879"></a><tt class="py-lineno">879</tt>  <tt class="py-line">                <tt class="py-comment">#pps = last_pps</tt> </tt>
<a name="L880"></a><tt class="py-lineno">880</tt>  <tt class="py-line">                <tt class="py-comment">#liks = last_liks</tt> </tt>
<a name="L881"></a><tt class="py-lineno">881</tt>  <tt class="py-line">            <tt class="py-comment"># Evolve chains</tt> </tt>
<a name="L882"></a><tt class="py-lineno">882</tt>  <tt class="py-line"><tt class="py-comment">#            while sum(self._R &lt;=1.2)&lt;self.nchains:</tt> </tt>
<a name="L883"></a><tt class="py-lineno">883</tt>  <tt class="py-line">            <tt class="py-name">theta</tt><tt class="py-op">,</tt> <tt class="py-name">prop</tt><tt class="py-op">,</tt> <tt class="py-name">pps</tt><tt class="py-op">,</tt> <tt class="py-name">liks</tt><tt class="py-op">,</tt> <tt class="py-name">accepted</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream._chain_evolution()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_chain_evolution"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._chain_evolution" class="py-name" href="#" onclick="return doclink('link-197', '_chain_evolution', 'link-197');">_chain_evolution</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">,</tt> <tt class="py-name">prop</tt><tt class="py-op">,</tt> <tt class="py-name">pps</tt><tt class="py-op">,</tt> <tt class="py-name">liks</tt><tt class="py-op">)</tt> </tt>
<a name="L884"></a><tt class="py-lineno">884</tt>  <tt class="py-line">            <tt class="py-comment">#storing log post probs</tt> </tt>
<a name="L885"></a><tt class="py-lineno">885</tt>  <tt class="py-line"><tt class="py-comment">#            print self.omega.shape,  pps.shape</tt> </tt>
<a name="L886"></a><tt class="py-lineno">886</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">omega</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">pps</tt> </tt>
<a name="L887"></a><tt class="py-lineno">887</tt>  <tt class="py-line">            <tt class="py-comment">#Compute GR R</tt> </tt>
<a name="L888"></a><tt class="py-lineno">888</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.gr_R()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#gr_R"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.gr_R" class="py-name" href="#" onclick="return doclink('link-198', 'gr_R', 'link-198');">gr_R</a></tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-name">j</tt><tt class="py-op">//</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L889"></a><tt class="py-lineno">889</tt>  <tt class="py-line"><tt class="py-comment">#            if sum(self._R &lt;=1.2)==self.nchains:</tt> </tt>
<a name="L890"></a><tt class="py-lineno">890</tt>  <tt class="py-line"><tt class="py-comment">#                print "Converged on all dimensions"</tt> </tt>
<a name="L891"></a><tt class="py-lineno">891</tt>  <tt class="py-line"><tt class="py-comment">#                print j, self._R</tt> </tt>
<a name="L892"></a><tt class="py-lineno">892</tt>  <tt class="py-line">            <tt class="py-comment">#Update last_lik</tt> </tt>
<a name="L893"></a><tt class="py-lineno">893</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">last_pps</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-comment">#on first sample</tt> </tt>
<a name="L894"></a><tt class="py-lineno">894</tt>  <tt class="py-line">                <tt class="py-name">last_pps</tt> <tt class="py-op">=</tt> <tt class="py-name">pps</tt> </tt>
<a name="L895"></a><tt class="py-lineno">895</tt>  <tt class="py-line">                <tt class="py-comment">#last_liks = liks</tt> </tt>
<a name="L896"></a><tt class="py-lineno">896</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L897"></a><tt class="py-lineno">897</tt>  <tt class="py-line">            <tt class="py-name">i</tt> <tt class="py-op">+=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt> </tt>
<a name="L898"></a><tt class="py-lineno">898</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">accepted</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">:</tt> </tt>
<a name="L899"></a><tt class="py-lineno">899</tt>  <tt class="py-line">                <tt class="py-name">ar</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-name">rej</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> </tt>
<a name="L900"></a><tt class="py-lineno">900</tt>  <tt class="py-line">                <tt class="py-name">rej</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">-</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">accepted</tt><tt class="py-op">)</tt> <tt class="py-comment">#adjust rejection counter</tt> </tt>
<a name="L901"></a><tt class="py-lineno">901</tt>  <tt class="py-line"><tt class="py-comment">#                print "==&gt; Acc. ratio: %2.2f"%ar</tt> </tt>
<a name="L902"></a><tt class="py-lineno">902</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">100</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt>  </tt>
<a name="L903"></a><tt class="py-lineno">903</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._tune_likvar" class="py-name" href="#" onclick="return doclink('link-199', '_tune_likvar', 'link-110');">_tune_likvar</a></tt><tt class="py-op">(</tt><tt class="py-name">ar</tt><tt class="py-op">)</tt> </tt>
<a name="L904"></a><tt class="py-lineno">904</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-200" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance" class="py-name" href="#" onclick="return doclink('link-200', 'trace_acceptance', 'link-4');">trace_acceptance</a></tt><tt class="py-op">:</tt> </tt>
<a name="L905"></a><tt class="py-lineno">905</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-string">"--&gt; %s rejected. Acc. ratio: %2.2f"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">rej</tt><tt class="py-op">,</tt> <tt class="py-name">ar</tt><tt class="py-op">)</tt> </tt>
<a name="L906"></a><tt class="py-lineno">906</tt>  <tt class="py-line">             </tt>
<a name="L907"></a><tt class="py-lineno">907</tt>  <tt class="py-line">             </tt>
<a name="L908"></a><tt class="py-lineno">908</tt>  <tt class="py-line">            <tt class="py-comment"># Store accepted values</tt> </tt>
<a name="L909"></a><tt class="py-lineno">909</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">c</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-name">pr</tt><tt class="py-op">,</tt> <tt class="py-name">acc</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nchains</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">theta</tt><tt class="py-op">,</tt> <tt class="py-name">prop</tt><tt class="py-op">,</tt> <tt class="py-name">accepted</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#Iterates over the results of each chain</tt> </tt>
<a name="L910"></a><tt class="py-lineno">910</tt>  <tt class="py-line">                <tt class="py-comment">#if not accepted repeat last value</tt> </tt>
<a name="L911"></a><tt class="py-lineno">911</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">acc</tt><tt class="py-op">:</tt> </tt>
<a name="L912"></a><tt class="py-lineno">912</tt>  <tt class="py-line">                    <tt class="py-comment">#Add something to the seqhist so that they all have the same length</tt> </tt>
<a name="L913"></a><tt class="py-lineno">913</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-201', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L914"></a><tt class="py-lineno">914</tt>  <tt class="py-line">                        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-202', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L915"></a><tt class="py-lineno">915</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L916"></a><tt class="py-lineno">916</tt>  <tt class="py-line">                        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-203', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-204', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L917"></a><tt class="py-lineno">917</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L918"></a><tt class="py-lineno">918</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">history</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">t</tt> </tt>
<a name="L919"></a><tt class="py-lineno">919</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.seqhist" class="py-name" href="#" onclick="return doclink('link-205', 'seqhist', 'link-6');">seqhist</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L920"></a><tt class="py-lineno">920</tt>  <tt class="py-line">                    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L921"></a><tt class="py-lineno">921</tt>  <tt class="py-line">                        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">pr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">t</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">else</tt> <tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">point</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">point</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pr</tt><tt class="py-op">]</tt> </tt>
<a name="L922"></a><tt class="py-lineno">922</tt>  <tt class="py-line">                        <tt class="py-name">ptheta</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L923"></a><tt class="py-lineno">923</tt>  <tt class="py-line">                    <tt class="py-keyword">except</tt> <tt class="py-name">IndexError</tt><tt class="py-op">:</tt> </tt>
<a name="L924"></a><tt class="py-lineno">924</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-string">"index error"</tt><tt class="py-op">,</tt>  <tt class="py-name">j</tt><tt class="py-op">,</tt>  <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L925"></a><tt class="py-lineno">925</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-206', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">liks</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L926"></a><tt class="py-lineno">926</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">j</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">samples</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt><tt class="py-keyword">break</tt> </tt>
<a name="L927"></a><tt class="py-lineno">927</tt>  <tt class="py-line">                    <tt class="py-name">j</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> <tt class="py-comment">#update accepted samples counter</tt> </tt>
<a name="L928"></a><tt class="py-lineno">928</tt>  <tt class="py-line">             </tt>
<a name="L929"></a><tt class="py-lineno">929</tt>  <tt class="py-line">            <tt class="py-comment"># Remove Outlier Chains</tt> </tt>
<a name="L930"></a><tt class="py-lineno">930</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">j</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt> </tt>
<a name="L931"></a><tt class="py-lineno">931</tt>  <tt class="py-line">                <tt class="py-name">outl</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream._det_outlier_chains()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#_det_outlier_chains"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream._det_outlier_chains" class="py-name" href="#" onclick="return doclink('link-207', '_det_outlier_chains', 'link-207');">_det_outlier_chains</a></tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L932"></a><tt class="py-lineno">932</tt>  <tt class="py-line">                <tt class="py-name">imax</tt> <tt class="py-op">=</tt> <tt class="py-name">pps</tt><tt class="py-op">.</tt><tt class="py-name">tolist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-name">pps</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L933"></a><tt class="py-lineno">933</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">outl</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L934"></a><tt class="py-lineno">934</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> </tt>
<a name="L935"></a><tt class="py-lineno">935</tt>  <tt class="py-line">                        <tt class="py-name">theta</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">theta</tt><tt class="py-op">[</tt><tt class="py-name">imax</tt><tt class="py-op">]</tt> </tt>
<a name="L936"></a><tt class="py-lineno">936</tt>  <tt class="py-line">                        <tt class="py-name">prop</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">prop</tt><tt class="py-op">[</tt><tt class="py-name">imax</tt><tt class="py-op">]</tt> </tt>
<a name="L937"></a><tt class="py-lineno">937</tt>  <tt class="py-line">                        <tt class="py-name">pps</tt> <tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">pps</tt><tt class="py-op">[</tt><tt class="py-name">imax</tt><tt class="py-op">]</tt> </tt>
<a name="L938"></a><tt class="py-lineno">938</tt>  <tt class="py-line">                        <tt class="py-name">liks</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">liks</tt><tt class="py-op">[</tt><tt class="py-name">imax</tt><tt class="py-op">]</tt> </tt>
<a name="L939"></a><tt class="py-lineno">939</tt>  <tt class="py-line">             </tt>
<a name="L940"></a><tt class="py-lineno">940</tt>  <tt class="py-line">            <tt class="py-name">el</tt> <tt class="py-op">=</tt><tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-208" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-208', 't0', 'link-188');">t0</a></tt> </tt>
<a name="L941"></a><tt class="py-lineno">941</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">el</tt><tt class="py-op">)</tt><tt class="py-op">%</tt><tt class="py-number">10</tt> <tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">el</tt><tt class="py-op">&gt;</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">j</tt><tt class="py-op">&gt;</tt><tt class="py-number">100</tt><tt class="py-op">:</tt><tt class="py-comment">#j%100 == 0 and j&gt;0:</tt> </tt>
<a name="L942"></a><tt class="py-lineno">942</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_acceptance" class="py-name" href="#" onclick="return doclink('link-209', 'trace_acceptance', 'link-4');">trace_acceptance</a></tt><tt class="py-op">:</tt> </tt>
<a name="L943"></a><tt class="py-lineno">943</tt>  <tt class="py-line">                    <tt class="py-keyword">print</tt> <tt class="py-string">"++&gt;Acc. %s out of %s. Acc. ratio: %1.3f"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">ar</tt><tt class="py-op">)</tt> </tt>
<a name="L944"></a><tt class="py-lineno">944</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler._watch_chain" class="py-name" href="#" onclick="return doclink('link-210', '_watch_chain', 'link-115');">_watch_chain</a></tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L945"></a><tt class="py-lineno">945</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-211" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.trace_convergence" class="py-name" href="#" onclick="return doclink('link-211', 'trace_convergence', 'link-5');">trace_convergence</a></tt><tt class="py-op">:</tt> </tt>
<a name="L946"></a><tt class="py-lineno">946</tt>  <tt class="py-line">                    <tt class="py-keyword">print</tt> <tt class="py-string">"++&gt; Likvar: %s\nBest run Likelihood:%s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likvariance</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-212', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L947"></a><tt class="py-lineno">947</tt>  <tt class="py-line">                <tt id="link-213" class="py-name"><a title="trunk.BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-213', 't0', 'link-188');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L948"></a><tt class="py-lineno">948</tt>  <tt class="py-line"><tt class="py-comment">#            print "%s\r"%j</tt> </tt>
<a name="L949"></a><tt class="py-lineno">949</tt>  <tt class="py-line">            <tt class="py-name">last_pps</tt> <tt class="py-op">=</tt> <tt class="py-name">pps</tt> </tt>
<a name="L950"></a><tt class="py-lineno">950</tt>  <tt class="py-line">            <tt class="py-comment">#last_liks = last_liks</tt> </tt>
<a name="L951"></a><tt class="py-lineno">951</tt>  <tt class="py-line">            <tt class="py-name">last_prop</tt> <tt class="py-op">=</tt> <tt class="py-name">prop</tt> </tt>
<a name="L952"></a><tt class="py-lineno">952</tt>  <tt class="py-line">            <tt class="py-name">last_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">theta</tt> </tt>
<a name="L953"></a><tt class="py-lineno">953</tt>  <tt class="py-line">            <tt class="py-name">ar</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-name">rej</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> </tt>
<a name="L954"></a><tt class="py-lineno">954</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt> <tt class="py-op">==</tt><tt class="py-number">2</tt> <tt class="py-keyword">and</tt> <tt class="py-name">j</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">10</tt><tt class="py-op">:</tt> </tt>
<a name="L955"></a><tt class="py-lineno">955</tt>  <tt class="py-line">                <tt class="py-comment">#print len(self.liklist),j</tt> </tt>
<a name="L956"></a><tt class="py-lineno">956</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="trunk.BIP.Bayes.Melding.Meld.current_plot" class="py-name" href="#" onclick="return doclink('link-214', 'current_plot', 'link-118');">current_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.best_prop_index" class="py-name" href="#" onclick="return doclink('link-215', 'best_prop_index', 'link-119');">best_prop_index</a></tt><tt class="py-op">,</tt> <tt id="link-216" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-216', 'step', 'link-59');">step</a></tt><tt class="py-op">=</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L957"></a><tt class="py-lineno">957</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.term_pool" class="py-name" href="#" onclick="return doclink('link-217', 'term_pool', 'link-26');">term_pool</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L958"></a><tt class="py-lineno">958</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">ptheta</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L959"></a><tt class="py-lineno">959</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_phi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">burnin</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L960"></a><tt class="py-lineno">960</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">post_theta</tt> <tt class="py-op">=</tt> <tt class="py-name">ptheta</tt><tt class="py-comment">#self._imp_sample(self.meld.L,ptheta,liklist)</tt> </tt>
<a name="L961"></a><tt class="py-lineno">961</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt class="py-name">likmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-218" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.liklist" class="py-name" href="#" onclick="return doclink('link-218', 'liklist', 'link-7');">liklist</a></tt><tt class="py-op">)</tt> </tt>
<a name="L962"></a><tt class="py-lineno">962</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">meld</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-219', 'DIC', 'link-16');">DIC</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.DIC" class="py-name" href="#" onclick="return doclink('link-220', 'DIC', 'link-16');">DIC</a></tt> </tt>
<a name="L963"></a><tt class="py-lineno">963</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Total steps(i): "</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-string">"rej:"</tt><tt class="py-op">,</tt><tt class="py-name">rej</tt><tt class="py-op">,</tt> <tt class="py-string">"j:"</tt><tt class="py-op">,</tt><tt class="py-name">j</tt> </tt>
<a name="L964"></a><tt class="py-lineno">964</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"&gt;&gt;&gt; Acceptance rate: %1.3f"</tt><tt class="py-op">%</tt><tt class="py-name">ar</tt> </tt>
<a name="L965"></a><tt class="py-lineno">965</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC._Sampler.shut_down" class="py-name" href="#" onclick="return doclink('link-221', 'shut_down', 'link-104');">shut_down</a></tt><tt class="py-op">(</tt><tt class="py-string">'Finished normally.'</tt><tt class="py-op">)</tt> </tt>
<a name="L966"></a><tt class="py-lineno">966</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div></div><a name="L967"></a><tt class="py-lineno">967</tt>  <tt class="py-line"> </tt>
<a name="L968"></a><tt class="py-lineno">968</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L969"></a><tt class="py-lineno">969</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
<a name="L970"></a><tt class="py-lineno">970</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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